Just to back up some of the stuff I wrote earlier...
This is the report that Melanie Phillips referred to:
http://www.diis.dk/graphics/Publications/WP2006/DIIS WP 2006-7.web.pdf
It is prima facie credible and makes for interesting reading on the IHH and the wider nexus between Islamic charities and militant Islam.
This is the IDF recording with radio chatter from their onlookers:
Broadly it backs up the Israeli version of being attacked by the protesters.
More specifically it verifies Israeli claims that the soldiers were principally armed with paintball guns - at 1.01-1.03 on the recording you can clearly make out a the hopper of the paintball gun as the soldier levels his weapon.
This video appears to show roughly the same timeframe as the one above except from the angle of those on the deck - i.e. the initial moment of boarding:
It appears to show an Israeli soldier being stabbed, albeit with a small blade, possibly a kitchen knife. The general impression is of a melee.
A final point, there appears also to have been at least one activist who was recorded wearing a gas-mask while in and around the central scenes.