a16z is almost certainly doesn't own a majority of GitHub, so it's not entirely their decision.
I think it's about trying to take the question of acquisition off the table completely. The people who put money in to a16z's fund might be unhappy if they turned down an offer. The other people/groups (employees and angel investors) who hold shares of GitHub might be unwilling to turn down a big payout, when, in this case, a16z wants GitHub to keep existing and working closely with them. If the company is essentially overvalued from this investment, no one's going to make that offer.
To your point, I don't see how that benefits GitHub's management, though, unless they value independence over profit (which is entirely possible, but I have no idea).
I think it's about trying to take the question of acquisition off the table completely. The people who put money in to a16z's fund might be unhappy if they turned down an offer. The other people/groups (employees and angel investors) who hold shares of GitHub might be unwilling to turn down a big payout, when, in this case, a16z wants GitHub to keep existing and working closely with them. If the company is essentially overvalued from this investment, no one's going to make that offer.
To your point, I don't see how that benefits GitHub's management, though, unless they value independence over profit (which is entirely possible, but I have no idea).