In Iron Man 2, Tony spends a lot of time fighting Rhodey in the Stark mansion right after he had a party. Since the Mk2 is still run by J.A.R.V.I.S, couldn't he simply ask J.A.R.V.I.S to shut it down? Why didn't he do that/think of that? He was inebriated, true. But still, Stark is sharper when drunk than most men are when they are completely sober.
Given that the armor's controlling software had been edited by Vanko and a backdoor was installed, I expect that any backdoor Tony had was closed by Vanko.
We also never see War Machine or Iron Patriot talking to J.A.R.V.I.S., so it's possible that that armor (which, if you recall, Stark had intended for Rhodes to have) was running a stripped-down version of the OS.
Earlier, when Rhodes had just stolen the Iron Man armor, Tony was supremely drunk. When you are drunk, even when you're Tony Stark, you tend to focus on one thing to the exclusion of all else. Tony focused on beating up Rhodes. He probably didn't want to order J.A.R.V.I.S. to shut it down or kick him out - then Tony couldn't have fought Rhodes, he would have just killed him (which Tony, even drunk, didn't want).
Keep in mind, though, that Tony wanted his friend to have the armor. Rhodes had security access to the vault, was an authorized user for the armor, and it was set up for immediate use. Tony could likely have kicked Rhodes out of the armor (had he wanted to and been sober enough to consider it) but he didn't truly desire to do so. In his mind, fighting for the armor (and learning how to use it in the process) would make Rhodes better at using it to fight evil (recall, Tony was certain he was going to die soon) and less likely to hand it over to others. Basic psychology: the harder you fight for something, the less willing you are to give it up.