Because that would be altering game mechanics, which cannot be done without extreme hacking and tampering of the game's code. Banning Swagger is something that can be easily implemented in cartridge play, while removing secondary effects is not.
The difference is arbitrary because we don't play on a cartridge. Why would it matter to Showdown whether a rule change would require hacking an X/Y cartridge or not?
Personally I'd be in favor of that Ice Beam part. Nobody likes being frozen.
Because at some point you are not playing pokemon anymore. You made it so different that is no longer the game that got people hooked up in the first place.
And that is subjective. What is "not Pokemon" to you could be "still Pokemon" to someone else. I've met people (and I'm not one of them) who've insisted that Smogon's clauses, as they are now, makes simulators a totally different game from the cartridge.