It was their friends from Book's community.
From the movie script (available on the Internet Movie Script Database and also here):
Mal comes striding out, where the crew have been gathering bodies, laying blankets over them.
MAL: Get these bodies together.
ZOE: We got time for gravedigging?
MAL: Zoe, you and Simon are gonna rope 'em together. Five or six of 'em. I want them laid out on the nose of our ship.
SIMON: Are you insane?
KAYLEE: What do you mean, the bodies...
MAL: Kaylee, I need you to muck the reactor core, just enough to leave a trail and make it read like we're flying without containment, not enough to fry us.
KAYLEE: These people are our friends --
If it was the Alliance soldiers, they wouldn't have been laying out the bodies neatly and covering them with blankets - they would have given those killers a mass grave at the very best. Furthermore, Kaylee says "These people are our friends", referring (it seems, judging from her previous words before Mal interrupted her) to the bodies.
In an earlier take of the same scene, Mal explicitly said that Book himself should take a prominent position on the nose of Serenity:
MAL: Put Book front and centre. He's our friend, we should honour him.
You can see this take at about 5:00 in the following blooper video, in between a lot of clips of Nathan Fillion being hilarious and Summer Glau being blamed: