... reality guarantees that guarantee cannot happen. It doesn't take GM products to have that sort of mutation occur. Makes it more likely and/or more rapid, I guess? But it's not like existent less!GM crops are some kind of weird indefinitely static... thing. They also change, the bacteria involve change, etc., etc., etc. Your profs appear to be complaining about a process that already exists and that GM is not introducing, which makes it kinda' weird to be focusing their tirade against GM.
The difference between evolution and GM is that the former reacts, and the latter acts.
There is indeed no guarantuee that, in the example case of pesticides, resistant soil bacteria, or resistant weed species will evolve through process of random mutation and natural selection. Our tendency for monoculture (relative to natural biodiversity) and extensive use of (only a select few types of) pesticides probably have increased the probabilty of this happening by increasing selective pressure. Still, evolution is usually a process of 10s of thousands, if not millions of years, and seeing how very short our species has been using pesticides, on a evolutionary timescale, it is not very likely that we would see this happen within our, or our children's lifetimes, at least not on an uncontrollable scale.
However, if geneticists actively tailor genes, specifically deisgned to provide resistance against commonly used pesticides, knowing that there are already existing organisms in nature that can basically copy-paste genes, it is like handing it to said organisms on a gold platter, especially if you proceed to go about distributing your GM product to every niche on the globe were it can economically be grown. If evolution would throw us a similar mutation, it would probably start very local, and be more containable.
... beyond that, again, there's a lot more to GM than the pesticide related stuff. If folks are really going to get in a panic about that, just legislate specifically against that and leave all the other good stuff be instead of just blanket condemning the lot of it.
There probably are some modifications that I would be willing to agree on being harmless. I just feel that that classification should only be made by cynical and pessimistic biologists, who look at everything from a worst case scenario perspective. It should never be decided by economic interest.
Horizontal gene transfer between two eukaryotes is very, very, very rare though.
Knowledge of soil microbial life is only now starting to catch up from being a very undeveloped section of our scientific database of life on our planet.
Who knows, down there it might be less rare than we think.