Yes the accident with the mutagen was partly his fault. That doesn't mean it wasn't traumatic, though. Some people react badly to strange or unpleasant situations and look for someone to blame. Even April was mad at the turtles for awhile after her father mutated.
If Timothy were cured, it's not unreasonable to think that he might be a little unnerved by all that had happened since he met the turtles and that he would choose to stay away from them for some time.