How a judge would fix it could vary from situation to situation. As such, it's impossible to offer you any definitive answer here. Perhaps the judge would say he cast the bolt on the face-up Angel, perhaps the judge would say he tried to do something he couldn't and rewind it. The specific details of each situation mean the results might be different. (And no, this is not an invitation to follow up by attempting to provide what you consider to be every relevant detail to get an answer to this specific situation. For all the relevant details to be available, the judge needs to be there, and how one specific situation would be handled isn't a discussion that helps anyone, since the next situation won't be exactly the same.)
For reference:
702.35d If you have priority, you may turn a face-down permanent you control face up. This is a special action; it doesn't use the stack (see rule 115). To do this, show all players what the permanent's morph cost would be if it were face up, pay that cost, then turn the permanent face up. (If the permanent wouldn't have a morph cost if it were face up, it can't be turned face up this way.) The morph effect on it ends, and it regains its normal characteristics. Any abilities relating to the permanent entering the battlefield don't trigger when it's turned face up and don't have any effect, because the permanent has already entered the battlefield.
So, I know in comp rules it states that morph is a static ability creating a special action and does not use the stack. The issue is whether or not opponent gets to keep their lightning bolt and untap their land due to reversing an illegal play (response to a morph). The opponent wasn't very specific about what he was responding to...
I just want to know how a judge would fix this. Opponent calls the judge when I won't put my angel in yard because morph doesn't use stack and he can't respond to flips...