True, there really aren't 100% counters to Murkrow, but Porygon can only switch in safely on one Murkrow set. I don't know if it's just me, but that definitely isn't "checking Murkrow" when any other set can beat it. Now if we look at other Murkrow checks they include:
Aron, which isn't 2HKO'd by Life Orb Mukrow unless it carries Hidden Power Ground over Grass / Dark Pulse. It beats Toxic + Taunt Murkrow, as well as Sub-Roost Murkrow and Choice Scarf Murkrow. Probably loses to Parafusion more often than not (but it probably has a better chance of winning than Porygon) and will likely lose to Clam Mind Murkrow.
Tirtouga, comfortably checks Choice Scarf Murkrow and it can beat Taunt + Toxic Murkrow as well. Sub-Roost sets are easy switch ins, and I'm sure there was an EV spread posted that could actually survive Hidden Power Grass from Life Orb Murkrow with Solid Rock if you are using a bulkier set. Probably loses to Parafusion but again, it has a better chance than Porygon. Also probably loses to Clam Mind Murkrow with smart play, but Stone Edge does have a high critical hit chance.
Archen, beats Life Orb Murkrow quite comfortably, checks Choice Scarf Murkrow very well, beats Sub-Roost with little problems, as well as Taunt + Toxic Murkrow. Parafusion Murkrow probably wins, as well as Calm Mind Murkrow.
Hippopotas, loses to Life Orb, beats Choice Scarf, beats Sub-Roost, loses to Taunt + Toxic, beats Calm Mind if it has Toxic or Whirlwind, and will probably beat Parafusion as long as it has Rock Slide.
Magnemite, loses to Life Orb, beats Sub-Roost, does decently against Choice Scarf I suppose, beats Taunt + Toxic, Parafusion is iffy, but again, it has a better chance than Porygon. Calm Mind is a toss up. If it has Dark Pulse, it loses. If it has Hidden Power Flying, it will probably win.
Chinchou, loses to Life Orb pretty much. beats Sub-Roost, beats Choice Scarf, and beats Taunt + Toxic if it's offensive, loses if it isn't. Wins against Parafusion, and loses to Calm Mind.
All of them perform better than Porygon. Can they beat every Murkrow set? No. But they can handle more than one, which makes them decent checks. Porygon wins against one set and one set only, which really doesn't make it a check to Murkrow.
Also, Toxic on Porygon really isn't that good, as Bronzor, Ferroseed, and Pawinard don't care about it. It's really only for Lileep, but you'll open yourself up to Tirtouga, Omanyte, and Shellder, so it really isn't worth it.
And because Choice Scarf Murkrow uses a +Attack Nature, it can definitely 2HKO Porygon:
240+ Atk Murkrow Brave Bird vs. 236 HP / 196+ Def Eviolite Porygon: 10-13 (38.46 - 50%) -- 59.38% chance to 2HKO after Stealth Rock