A couple people have run into problems with Magic Barrier when the levels they learned and bonus levels added up to 5 or more, but I don't recall any issue with bonuses boosting the skill higher than you can learn yourself.
Try using
iZakaroN's SaveEditor (or from
Kiya's site, with description) to remove the skill points you put into Magic Barrier, then reload that save and see if you can unequip the items without a resistance drop.
You can use the save editor to boost your resistances back to normal. Since the resistance bonus is added when you learn the skill level, you can repeatedly learn and unlearn the skill. Boost Magic Barrier and save, use the save editor to remove the skill points, re-load the save, re-learn the skill and save, and repeat as necessary.
Resistances can also be edited directly, if you are comfortable hex editing. See
Some more hex offsets... and also
Teleporting Anywhere, via hex editor as a reference.
If you wish to get rid of the equipment you have with a Magic Barrier bonus, but don't have anything comparable in quality, you can use
DAD's item editor to duplicate their stats (minus the skill bonus) on other equipment.