Purely from a feature development perspective, I guess I don't see how adding a read-it-later / bookmarking feature would generate so much consternation. Functionally its roughly equivalent to Reading List + Bookmarks on Safari, with some delicious-like aggregate smarts.
Would it have been better to have built it internally instead of through acquisition? I admit I'm unfamiliar with the inside baseball on it's integration, but breach of trust sounds pretty drastic. My read (as an uninformed outsider) is that they probably acquired Pocket for a song, it filled a gap in the product offering, and it offers the potential of a future optional revenue stream that aligns well with the web as a document reading medium (subscription).
There's all sorts of internal browser features you can't 'completely remove'. How is bookmarking different?