I missed today's stage, and I have no time to watch it. From what you are saying, some people protested the Israeli team by blocking their progress. I know of no set rule regarding protests. There are clear rules about stoppages due to outside influences, in particular, at a railroad crossing. In that case, if the gap is less than 30 seconds, it's a racing incident, and tough luck. If it's more than 30 seconds, then the group or groups up the road are neutralized until the race can be restarted. At the restart, all gaps are put back in place, and the race resumes.
So let's say that I'm a UCI commissaire (I'm not) and I'm on the jury. Let's also say that the protest lasted 2 minutes before the riders could restart. Let's also assume that no individual rider got away, and that the IPT team restarted with a minimum of 3 riders (I don't know if this is true or not as I didn't watch it). I am 99.9% sure that there was a UCI motor commissaire with the team, and that they started a watch when the team was impeded. I am 90% sure that they stopped that watch when three riders started racing again. My vote at the jury would be to take their finish time off the third riders wheel, subtract the time lost at the protest, and add 30 seconds. This is the UCI though, so who knows.