No one had my suggestion so I'll throw my idea in 'cause I've had that same thing. My solution is to temporarily fleet 'em. Simple yet effective 'cause ships in a fleet don't show up in the retro fit queue.
If they're already fleeted, just remove the ships from that fleet you want to retrofit, do the deed and put 'em back in. They still get repaired if they're in a fleet, don't loose any ship or fleet experience, etc. etc. - I find no downfalls about it.
If you try it a little, you'll see what I mean - especially when you have 150+ ships in the sector. Every place I do retrofits, I always have temp fleets; preRetrofitXX and postRetrofitXX and that keeps my retrofit queue clean, lean, and mean.
