The party's few remaining thinkers remain influential and cannot abide Trump. They'd rather support an independent conservative than vote for him.
I think they would put up with Cruz, assume he will lose and wait for a better candidate at the next election. Meanwhile, they will hope to retain the House and Senate and block anything they dislike that is proposed by the Democratic President, which is nearly everything.
They will likely expect a Trump candidacy under an independent banner if Cruz wins. But I expect they will assume he costs the party one election. Will he return in 2020? Probably not. Too much wasted time for the man with a brand to work on.