I can see how the biology analogy could lead itself to preordained outcome, but I do not think it was the case in this research. For one it is really just a biology analogy, the mathematics are standard graph theory/statititical mechanics. Actually, the original results we got back from the simulations had mass network failure occuring when 23-24% of nodes were compromised, all being of the same species. Ended up we had a flaw in the code, but with that result you could not really argue that monopolies cause a security vulnerbility. It would be impossible to enforce a mandate saying no one vendor could have more 23% of market. The conclusion would be that even with a thriving competitive market vendor specific vulnerbilites can do heavy damage. Going after Microsoft or any other quasi monopoly in this case would not accomplish much. If you look at code red affecting microsoft servers, they only made up 23-24% of servers connected to the Internet at the time (and that was all MS....
I will say it is easy to fall into the politically biased trap, especially as more people pay attention to what you are doing, but it is something we try hard to stay away from. Sorry if this has wandered of topic in that regard.
As an aside it is interesting that no worm has yet exploited a platform that has a large market share and is at the core of the network.