My theory is that it was Revan who shot HK-47, because when Revan told HK-47 that he/she is going alone into the unknown regions, HK probably was very stubborn and would have refused to part ways with Revan (even though Revan is his master) so the only way to prevent HK-47 from going with him/her into the unknown regions was to use force, hence, he/she shot HK-47, well that's my take on it, it makes sense in my book.
<{POST_SNAPBACK}>
Revan shooting HK-47? I thought that it was plainly obvious in the prologue that the HK-50 you encounter on peragus busts into the cargo hold and shoots HK-47. And remember that during the prologue you can go to the cargo hold and hear a banging noise which should be evident that HK-47 is still intact.
<{POST_SNAPBACK}>
Unless it was HK-50 who banged and banged on the door...