It won't cause issues if you plug any holes that it leaves in your hull properly after removal. You will have to find a place for the VHF and Nav lights though. Would be much better to get someone to hinge the frame from the front and have a clamp arrangement from the back so that it can be folded down. Or just remove some height from the frame by lopping off what you need from the bottom of the tubes and rewelding the feet on. Just remember to make an allowance for the tilt of the outboard.
Looks Slow but is Fast
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Yes you can remove the A-frame. Make sure you seal the holes up though. You'll need to reposition the VHF and GPS antenna too - this is not ideal (especially the VHF - you want to get as high as possible). Not sure if there are Nav lights to deal with too?
You can reengineer the a-frame to make it fold - which is another option (but needs to be done properly or you'll have a disaster on a big wave one day).
As an alternative can you lift the bow enough (think extra long jockey wheel) to make the back dip? Depending how far you tow it might also be practical to fit smaller wheels?