Plenty of members of the team were having second thoughts from the start. And they made a point a few times about how the information linking the suspects to the bombings was secret intelligence, and not necessarily true. And how that, in killing the leaders, they just brought new harder-line leaders in and caused more killing down the line. It was definitely a bit too long, and the Bana-having-sex-with-his-wife/Israeli-athletes-getting-shot-up-for-the umpteenth-time was pretty ridiculous. Definitely not "Israeli propaganda" though, Spielberg just likes to hit the emotions again and again.