I think McConnell and the establishment wing of the party always felt like Moore would not be a great fit for what they want to do. He's a bit of a loose cannon, might chafe at following marching orders, and generally behaves like the kind of a caricature that liberals might draw to try and defame conservatives, which reflects poorly on the party when they want to court the ever-growing independent voting bloc. He also defeated the primary opponent they all wanted.
But, what to do? They're stuck with him, if the voters choose, right? Well, with these revelations, not so much. If these allegations are true, most people generally consider that to be behavior not meeting the standards of a public servant, so they would have an opening to expel him if they want. By advertising that he'd think Moore is unfit, and that they'd probably expel him, it sends a message to Alabama Republican voters (the strong majority in that state) who might find the accusations against Moore credible. That message is (not an actual quote, BTW)-
Don't elect the Democrat. We'll take care of Moore, so you can elect
him, we'll throw him out, and the governor will be able to appoint a
temporary replacement, then we can have another special election and
elect another Republican (possibly even the original, Sessions, if
he's done being the Attorneys General). If you stay at home or vote
for Jones, then the Democrat will hold the seat until 2020.
It would have the added side benefit of the GOP being able to claim that they took the almost unheard of (for either party) step of putting aside partisan considerations to do what's right by expelling one of their own who just won an election. This would greatly enhance their reputation and standing with independent and younger voters, even if there were accusations of more cynical motives (which could easily be turned around on accusers, who would be painted as complaining that they did the right thing).
So, the GOP could get the kind of person they always wanted for that seat. They can push back on accusations that they are the kinds of misogynists who would not believe (without extraordinary proof) women who accuse powerful white men of abuse or harassment. They can claim the mantle of taking the most pro-woman actions possible for the situation. And because of these side issues, people are going to help, not oppose them, in getting their more favored (by the party and leadership) person into that seat.
If he's elected, and they act to remove and replace him, it could wind up being a huge boon for the party. Given that set of circumstances and all the advantages, I think it would be highly unlikely that the GOP would not remove him, which is why I didn't directly address the last sentence of your question as much as deal with how they can use the situation to their advantage.