absolutely collaboration and cooperation can be harmful in themselves. arguably all the individualists are complaining about that very thing (among others). it seems many people fall into "getting along to get along", stop thinking for themselves, accept the assumptions and criteria of their group or their friends without interrogating them (interrogating the ideas, not the people--although interrogating people can be fun too ;) ), etc. (which is the point of the "annihilation of others" that you note).
so if you're defining collaboration and cooperation as always being between people who are well individuated, not afraid to be in conflict with each other, understand their differences as well as their similarities, then sure, it can be fun and productive. but no one is like that all the time and some people are almost never like that.
i find that there is a lot less trust involved in competition than there is in cooperation and collaboration. that alone leaves the latter open to more intricate situations of potential positive and negative experiences.
of course cooperation and collaboration can have negative and/or positive aspects and outcomes, depending on the situation and the folks involved. just as can competition.
claiming something (eg, collaboration) as positive or negative in and of itself holds no interest for me; only in the context of a situation can i determine if i consider something as having positive and/or negative results/impacts. and almost always will there be some of both, if i look at it in a holistic sense.
i also agree with amorfati's comment above. "human progress" is not something i see as inherently "positive" (that is putting it mildly - i mostly feel the opposite). work, in the sense related to capitalism in particular, is something i can pretty much never see as "positive", since i despise and try to avoid as much as possible the capitalism that infuses far too much of the world i inhabit.