I'd say the most important difference is that 真面目 is mainly used in positive contexts, and 深刻 in negative. As in "he is a serious student" versus "the situation is serious."
To me, 深刻 sounds more serious than 真面目。
If you have 深刻な顔, you are most likely to have something on your mind. If you have 真面目な顔, you're having such a face simply because there's no funny thing happening.