Hi, I'm a former computer nerd, now a biologist.
Don't overestimate the role of mutation in short-term evolution. The rate of mutation per site per generation in almost all extant species is very low, and almost all mutations are deleterious. For any de novo allele to persist in a population, it must confer a significant benefit to survival or reproduction. If its selective benefit is only slight, its chance of persistence or fixation in a population is equal to its initial frequency, which is extremely low (except in very small populations, but then you have other problems). Mutation is certainly necessary for evolution, but it works on extremely long time scales.
From a biological standpoint, what Monsanto does is pretty irrelevant. They create populations that, barring mutation, don't reproduce. What they do does not affect the genetic variation of natural populations, except insofar as it restricts the total acreage occupied by non-GMO crops. But it's important to realize that those non-GMO crops are _not_ natural populations, nor are they "natural" plants. Such crops have been as thoroughly modified by man as has any Roundup-Ready plant. That's exactly what selective breeding for greater yield, better taste, etc. are - genetically modifying organisms. Corn, wheat, cabbage, mustard, and a whole host of other plants that are grown "organically" and eaten every day do not occur in nature in the forms we consume. The only difference is that companies like Monsanto target single genes, because they can. There is an argument to be made that, by selectively adding or modifying only beneficial alleles, biochemical engineering is a safer way to shape crop plants to our needs; selective breeding is sloppy, messy, and can't eliminate negative genes that, for example, are in linkage disequilibrium with selectively positive genes. And, if you don't want to grow GM seeds... don't. Agribusiness isn't preventing anyone from growing old crops the old way.
From what I have observed, most people's objections to Monsanto boil down to what one of my non-major humanities professors said: "It just doesn't seem natural." People don't seem to realize that when engineering these plants, what is happening is simply a refinement of a process that's been going on in agriculture since we first figured out planting seeds makes plants grow. It's just a more precise version, and able to avoid a whole host of problems presented by the old way of doing things. But it's happening in a lab, so it's automatically unnatural, and interfering with either God's plan or evolution. Evolution is a tricky subject, and far more complicated than most people realize.
I guess what I'm saying is, don't get a gut feeling about something and just call it good. There is a huge amount of propaganda on both sides of this issue, and the reality of the situation is more nuanced than 99% of people realize. I'm probably going to get attacked for this as a Monsanto shill, but please note that I didn't take a firm position either way. There's a reason for that: despite all the screaming from both sides, there is not enough reliable data available to do real, objective science on the broader effects of widespread GMO agriculture. Unfortunately, this dearth of data just feeds the gut feelings on both sides.
Lecture over. Feel free to flame.