Youk was out. If he didn't try to avoid the tag, he wouldn't have gone out of the baseline. If he was smart, he would have just stopped running. At the very least, A-Rod wouldn't have been able to turn the double play.
I don't know what was up with Joba, but keep in mind he hadn't gone more than an inning on one day rest since he's been up, so fatigue/lack of control is not all that unlikely. Regardless, for all the times Boston pitchers have hit Yankee players, Joba gets a pass. I don't have the stat on hand, but I know the numbers are at least 2 to 1 of Yankee players hit as opposed to Sox players hit. I just wish he made Ortiz move his feet in the box. Nobody has ever done that to him.
If the Sox won 1 game this series (which I pretty much expected them to do) I'd have been sure the division was wrapped up. Now with Ramirez out a week and a half, coming off a sweep with Tampa on the schedule, this is a race again. The Sox lineup is light years behind what it normally is when Manny isn't playing, and that could come back to bite them the next few games. The Yankees could very well shave a few games off and make this real close when they meet again in Fenway.