I would say no comma.
"He who contemplates, that is the philosopher, ..."
I understand that there is a pause betweeb the 'is' and 'the', but these two statements are closely linked. Perhaps you could use other punctuation if you wanted to keep the pause:
"He who contemplates - that is, the philosopher - ..."
Certainly, if you use 'i.e.' then no comma is needed:
"He who contemplates, i.e. the philosopher, ..."
i.e. means only 'that is' (id est, in Latin), so it is acceptable to use either. I wouldn't say i.e. is confined to formal documents either; it's not 'informal' but it wouldn't be out of place in an email to a friend, or whatever. Also, it isn't uncommon to hear people say 'i.e.' in speech.