I live in Allston now and have been in the mission hill area many times.
It is a fine area but I would follow some basic rules. I would not walk alone at night at 1 am unless there were many others walking about as well. Also, make sure you do NOT live on the ground floor (This goes for the Allston/Brighton area as well). People think it is hilarious to kick in windows or simply knock on your windows in the middle of the night....
But overall it is really not that bad just be aware of your surroundings etc.
About the T. I have been taken the T for two years now on the B green line, I also take the 66 to classes at harvard ext, I have never had any problems. Yes there are going to be crazy people from time to time but i have never felt like i was in physical danger. The only thing i dont like is the 66 is never on time....
