I recall a time when I was able to get paints without crystals, either by buying them with gold or crafting them. But it seems now they can only be purchased in packs for crystals. Is there any other way?

Well, there are other ways; earn crystal and get them for free:
-Wheel of four gods (very low chance, very low crystals, not enough to buy anything with it)
-Panzar Facebook (not sure if the weekly questions are still there, worth checking)
-Panzar Forum (sometimes there are events to earn some crystals by solving a puzzle etc)
-Playing tournaments (your best bet, if your class is not full, play in low level tournaments)

So... I definitely need crystals? They changed it from being able to craft them to (usually) having to pay real money for them?

Yes. As far as I know in most (if not all) of FTP games, you need to pay (atleast game's currency) for colors, themes, clothes, costumes etc.
You can earn crystals instead of buying. Paints are cheap and considered free compared to upgrades which needs loads of coins and lucky horseshoes.