Sounds like you might be misreading several things. First point, job boost potions level the appropriate job to 60, not 50 (may have been a typo on your part). But you are correct, the job boost potion would not affect any of your story progress, and you could continue leveling THM into BLM no troubles.

More important point though, is the cross class skills have been removed. Leveling CNJ will do you no good for gaining any CNJ skills on THM. You now have a list of role abilities to choose from. You do not get any Protect, but that's largely unnecessary for open world content; the mitigation is minimal, and you should be more than capable of burning things down before they pose any real threat (if you're having any particular trouble, you may need to be looking at upgrading gear, understanding your available skills [you've still got Sleep available] or potentially calling on your chocobo to fight for a little extra assistance).
Your only available self healing ability will be Drain, which should suffice in most cases to keep you alive and able to finish any particular mob. Still completely possible to be overwhelmed, but that's something Cure/Protect never would've helped with anyway.