It's still incredibly unfair if you like a Pokemon for its stats and movepool, and are forced to not use it just because it has a bad ability that you're not going to use. That's a massive load, and you know it.
And no, banning certain movesets and banning an ability on a Pokemon are not the same thing. At all.
You're right. Banning an ability on a Pokémon is worse.
Each Pokémon has, at most, three abilities. Some, such as Blaziken, only have two. And others, such as Flygon, only have a single ability. An Ability is one of the core aspects of a Pokémon. Restricting what abilities they can use are far worse than restricting which moves they can use, as it can eliminate part of what defines that Pokémon. If the ability itself is not broken, which Speed Boost is not, there is no reason to ban the Ability. By doing so, you would be making the "incredibly unfair" move of banning Ninjask, despite the fact that Ninjask with Speed Boost is not broken in the slightest.
Speed Boost itself is not broken, so it does not get banned. Speed Boost is also far, far more useful than Blaze (which Blaziken has neither the bulk nor the typing to do well with). Banning an Ability for a particular Pokémon is a silly attempt to keep an overpowered Pokémon in a tier where it does not belong.
Complex bans have been used, but only when there is no better option, as they are a slippery slope, and a poor precedent to set for the metagame. For example, despite the need for banning the Drizzle/Swift Swim combination, doing so has produced hundreds of posts saying "see, complex bans are good! This is exactly what we mean by it being a bad precedent. Complex bans are not a good solution, and I'll outline why in the three basic rules below.
Rule One: Never make a complex ban when a simple one will do. There was no simple ban solution possible for Swift Swim + Drizzle. Banning just Swift Swim would have essentially banned outright a number of Pokémon who had no other viable Ability options, and which were only broken in rain. Banning just Drizzle would have massively unbalanced the weather wars.
Rule Two: Do not make a complex ban unless it affects multiple Pokémon. If there was only one Pokémon that could use Swift Swim + Drizzle or Sand Veil effectively, that one Pokémon would have been banned instead of the combination. Speed Boost itself is not broken. Banning it would ban Ninjask and Scolopede, both of whom use it legitimately. This also helps avoid unnecessary complex bans, and leads into the third rule.
Rule Three: Do not make complex bans to keep a Pokémon OU. If you are banning a Pokémon, it is on the basis of its best ability. Sure, that Pokémon might be useless if it's run with only three moves or controlled by an unskilled player (such as myself). So what? This is a game of mathematics and metagame refinement (especially here at Smogon). Each Pokémon is taken to its pinnacle when determining sets and viability. Otherwise, we have a nasty precedent for things like "Deoxys-A is allowed in OU as long as it only carries two moves". If a Pokémon's best set is overpowered, that Pokémon is overpowered, and banned. We don't cripple it or remove its tools to keep it OU unless the tool itself is broken.
In short, Speed Boost is not broken, it is Speed Boost combined with Blaziken's stats, movepool, typing, etcetera. Banning Speed Boost would cripple otherwise decent Pokémon, and set a bad precedent for keeping Pokémon in OU that should not be there. Plus, all you would get out of it is a Pokémon who, without Speed Boost, is UU or RU at best, as Blaziken is otherwise not that impressive.
Read Rule Three. You don't create a complex ban for the sole purpose of keeping a Pokémon in a particular tier. We don't ban Magic Bounce Espeon to allow it into lower tiers, despite the fact that some people love Espeon and would use it without Magic Bounce (I ran Espeon on every team I've played since it was introduced, long before Magic Bounce). Heck, why don't we ban Drizzle Kyogre? Sure, it's Kyogre's only Ability, but without it, he's a lot more viable for standard play, and since the metagame is based on the simulator, it is within our power to control. We could create a Torrent Kyogre if we wanted. That's good.
Or, hey, why not ban particular Natures? We can unban Modest Blaziken, or Quiet Blaziken. It's not like a Special Attacking Blaziken is broken. So we'll do that.
The point is, once you start jumping through hoops just to keep a Pokémon viable, it never ends. You can make
any Pokémon viable if you put enough restrictions up.
All I know is, Blaziken is one of my favorite Pokemon. And it's a monstrous injustice that I can't use it just because an ability exists that I'm not using with it.
There are certain combos that should be banned, and that's not a problem. Swift Swim/Drizzle was one. Many will probably come to pass in the future.
It's not that complex when, listing bans, instead of "Blaziken", you just put "Speed Boost Blaziken". It's only two extra words, and people get it.
And the slippery slope argument never works. Ever.
Except, it does. As I pointed out, the Swift Swim + Drizzle ban has produced hundreds, if not thousands, of post suddenly arguing the benefits of complex bans. That is a perfect example of a bad precedent.
Espeon is my all time favorite Pokémon, and there were some calls to ban it in Gen V when it obtained Magic Bounce. If that had happened, I would play Ubers with Espeon. There is nothing stopping you from playing only Ubers and running Blaziken. There is, in fact, nothing stopping you from playing normally and using Blaziken. Smogon is a competitive community, and Blaziken is uncompetitive. So he is unavailable for competitive play. That is not going to change. This only, however, affects competitive play, and the Smogon community. Feel free to duel your friends, or ask people for matches, and play your own way.