We would expect the terms and conditions of your windscreen cover to explain how repairs or replacements are decided, but there is an argument that a repair that does not pass an MOT is not an adequate repair.

It may be that you can pay the small excess and have the repair, and if it fails the MoT you can than claim again, but your policy may have a clause limiting the amount of windscreen claims or requiring a larger excess. If you are unsure we would suggest contacting your insurers directly on this matter.