I usually always use CA glue unless the job calls for epoxy.
It sounds like your concern is more about damaging paint on parts you've already painted. 99% of the time some touch-up painting is required to cover glue bonds between two parts so scraping painted parts, if necessary, before joining them isn't a concern if done carefully. Once joined, touch it up with a fine sable hair brush and try to blend the brushed finish with the already painted finish.