Paint guns and weapons do not sound anything of the same. It is not as if IDF came firing deadly weapons and suddenly those on the ship were able to quickly dismantle rails and such as for protection. There is enough evidence to show those on the ship were well prepared ahead of time to do damage and perhaps deadly confrontation if they could. Previous raids did not begin or end this way.
Route 1 to Jerusalem reopened to traffic as fire outside of Jerusalem continues (Haaretz)
from the article: Blair hails deal with Netanyahu to ease Gaza blockade