I have no problem with God's pushing around molecules. I have no problem with finite persons' pushing around molecules.
I have little patience with the odd tendency among some Christian writers and thinkers to try to find space for mind-body interaction and even for miracles in, of all things, quantum theory. Or else, sometimes, we hear elaborate theories wherein God set things up by means of the Biggest Bank Shot Ever at the Big Bang so that He would never have to do anything ever after that involved actually reaching a hand down and touching matter. To be fair, these latter scenarios are usually applied only to God's making stuff, not to (say) Jesus' turning water into wine or raising Lazarus. But I can't see the principled difference. If it's so especially cool and important for God to set the initial conditions up at the Big Bang for, say, the origin of life, why wouldn't it be equally good for the miracle at Cana to be the result of a Big Bang bank shot, rather than an actual intervention? If the latter as a true intervention is not a problem theologically or aesthetically (or whatever it is that people worry about), why should the former be?
Why should it be a problem that God should intervene and bump something?
And really, let's just admit plain old mind-body interaction for humans, too, rather than trying to squeeze it in between quarks via quantum theory. Remember--that there can exist nothing but a closed physical system, or something that looks just like a closed physical system, is not a law of science but a metaphysical prejudice. Really.