... and that Naomi secretly gave Fred the location of the hidden proto-molecule torpedo?
Exactly this has not yet happened at the moment of the Fred-Holden conversation (S02E08); only in a later episode does Naomi give away the location of the protomolecule sample. And the protomolecule is indeed the motivation behind Fred's "hostility": Holden is heading to Ganymede to destroy it, but Fred wants a piece of it for himself/the Belt:
FRED: I don't have to let you leave, you know. With all the time and repairs I put into this ship, it's arguably more mine than yours.
HOLDEN: We just saved your life. Call it even.
FRED: I know we've had our differences. But if you find the protomolecule on Ganymede Station...
HOLDEN: I sure as hell ain't gonna bring it back to you.
FRED: Then don't bother to come back here at all.
Transcript from https://www.springfieldspringfield.co.uk/view_episode_scripts.php?tv-show=the-expanse-2015&episode=s02e08
Edit: While re-watching, I stumbled over the bit where Naomi tells Holden when she gave the location to Fred (in S02E13):
There was a moment on the Somnambulist when I thought I wasn't going to make it [...] I gave the protomolecule to Fred Johnson.