Correct, pagan rebels can only convert other pagans. You need to pull bankruptcy shenanigans to become pagan.
This has always annoyed me actually, because there's no reason for it. Only in fringe cases/for the lulz would you actually want to convert to pagan, where gold provinces turn into utter junk worth less than grain, multiple great power lucky nations get a giant across the world discount CB on you, your missionaries have junk for strength, and your alliances options are limited by different religions/powers that have exploration typically being hostile.
The only upside to being pagan is the stab boost for refusing to convert, which got nerfed in 1.8 because of DDRJake but is still useful.
Even the worst non-pagan religions for converting in the game cap out at 2 missionaries with 9% base strength (4% decisions, 3% religious) if you take religious ideas, 3rd missionary from Rome or a policy. Pagans cap at 5% strength (religious only), meaning that without positive stability or an inquisitor you can't convert a 3 tax Sunni province if it's wrong culture even with religious ideas.
If the logic was instead to prevent the player from accidentally being tossed into a bad religion, there was no logic at all lol. Even realism arguments don't work, because the game has no problems with stuff like Hindu Ireland, Sunni Knights or Castile, Catholic Ottomans, or Protestant Korea...which would make a realism argument as to why Mali for example can't go animist really awkward.
