In other words, there's no substantive difference between the survival-oriented alien invaders and human-built survival machines, so why bother to pre-emptively institute the outcome of invasion?

I doubt the premises. That assumes a very powerful kind of convergent evolution is at work - and that both parties have fully converged. Neither of which seem very plausible to me. Chance will result in different forms - and one civilisation may have got closer to perfection than the other.

If a modestly increased risk of destruction by aliens is compensated for by much greater achievement of our aims, why should we instead abandon our aims in order to create exactly the outcome we supposedly fear?

I take it that your goals do not involve avoiding all your distant descendants being systematically obliterated. If you don't care about such an outcome, fine. I do happen to care.

AI creating human uploads

I'm sceptical. I think uploads are harder than many think. I think that the motivation to develop the technology will be lacking (once we have AI) - and that relatively few people will actually want to be uploaded. Uploading makes no economic sense: there are easier ways to produce simulated humans. Finally, it's not clear to me that there will be many people left by the time uploading technology is eventually developed - and those that do finally get a glimpse of cyberspace from within will need complete personality transplants - if they want to stand a hope of holding down any kind of job.