Working with founders from acquired companies is not a great way to meet co-founders. First, many will have already "made it" and won't have the same drive that they once had. Second, if they do, they'll prefer to work (and socialize with) with other people who are like them -- other successful founders. Maybe they'll let you be an employee at their new startup.
Palantir is full of people who are itching to start a company, and we'll see dozens of startups by Palantir alums after Palantir exits (it's already happening; see posterous.com). The founders of these companies will have unique experience and connections in government and finance, giving them the option to target enterprise problems instead of entering the over-crowded consumer startup scene.
As far as reputation among Silicon Valley investors, having worked at Palantir will look at least as good as having worked at Facebook or Google over the next few years, especially now that Facebook and Google are already big and successful. Joining Facebook or Google today is relatively lazy; it's not as impressive to join a company that's already hugely successful as it is to join a company and contribute to making it successful. Assuming a choice between Palantir and Facebook, an entrepreneurial person with confidence in his/her ability to make a company successful will join Palantir.