I am thinking about joining the rebellion in skyrim. But if I join one side or the other will that restrict access to the other sides cities? If so I will remain neutral....
what will really get them roasting you is if you join the empire and then wack someone in an empire aligned city. Sweet talking your way out of stuff just got a whole lot more interesting!

But seriously,this shouldn't be a problem. Just be sure you don't commit any significant crimes like murder, or get busted for minor theft etc.
Also keep in mind each hold tracks your bounty separately. So if aligned with the other side, this might play a factor in your crime stats i.e. being with the imperial faction might make your bounty level more likely to rise faster in Riften. I suppose that's when being Thieves Guild master could come in real handy!