While skill checks as minor actions is good to avoid depircating skill checks as useless in combat, and are also good if a skill challenge represents a 'niggle' during combat, I think otherwise a skill use for a skill challenge that counts as a success needs to be a standard unless action.
Sure, your tanks can try to give some +2 bonuses to the real checks with minor use, but they shouldn't be both killing the monsters and solving the side-challenge too. Let your 'non-combatants' have some glory, or make it a tactical choice that your heavy hitters need to make to either deal with a creature directly, or solve the skill challenge (I assume this will help with the combat as a whole).
Along the lines of skill challenges as monsters, don't be afraid to have the success actually generate damage/status effects. The thief actually needs to trap his tools in the complex lock so becomes immobile, destroying the runes actually inflicts damage (or at least rolls an attack) for successfully disenchanting them. It makes the skill challenge not some boring thing you just roll for, but a tactical process itself. Does your healer need to support them or the fight, can secondary checks be used to increase your defenses or decrease damage, do you need a 'guard' PC to stop monsters taking advantage, etc.