I can't really say they are the favourite in winning the UEFA Champions league as you said,they have their main players injured and sold,Debruyne,Mahrez,Gundogan and Bernando Silva all out,but Pep has really shown that he is a very good coach,being able to device a means to win a team like Newcastle who have shown that they are worth their position last season.It makes me feel like he is the best coach in the world,but I still think a more organised team like Arsenal will win City if they should meet again when those players are out injured.
The champions league will soon start,and with the transfer window still on,most teams have the chance to add quality players to their squad ahead of the competition which will kick-off in two weeks time,and untill the game starts,we can't just conclude that City is the favourite for the Tittle.
In any case, at this moment in time, Pep Guardiola would prefer that De Bruyne was fine, rather than conducting urgent experiments on tactics to find a replacement for such a valuable player

In any case, Manchester City will be one of the main favorites of the current Champions League, but still its absence can play a negative role when it is necessary to solve the problem in a strictly defined match.