In my opinion the associated skills are the main problem concerning disciplines, I don't remember exactly but most of them would be keyed to Acrobatics due the way Paizo folded the skills and Diamond Mind even lost it's associated skills (autohypnosis works, but it "suffers" .that is is a Psionic only skill, at least as I can tell). For Prestige classes I think there wouldn't be much trouble besides adjusting the skill ranks requirement.
As far as mapping disciplines to the new classes I think that giving Devoted Spirit, &Iron Heart->Warder/Zealot, Diamond Mind & White Raven->Warlord and Shadow Hand & Setting Sun->Stalker/Harbringer(Maybe?) could work; Stone Dragon could again be an every-man discipline which everyone can pick, Desert Wind and Tiger claw overlap a bit much with new disciplines so I'm not sure, since Mystic apparently will have an "energy/magical" bent I guess Desert Wind could work for them.