How could he not have been prosecuted and condemned ? Pompey's soldiers were here to secure his conviction.
Pompey had been reconciled with the Claudii Pulchri since the conference of Lucca (his firstborn son married then Claudia Pulchra, Clodius' niece). He had no more reason to back Milo. In fact, since the renewal of the triumvirate, Milo worked for the optimates opposed to the triumvirate.
You are going to need many changes if you want Milo becoming consul in 52. First of all but not enough : not murdering Clodius.