Yes, in the episode the fight music does resume abruptly - there is no pause as heard on the GNP release. I happened to have this episode handy to check.
This is something worth noting as a whole on the set. Whilst the cues are presented as in the episodes they were made for, some are joined together, as they were in their intended episodes, as opposed to being 'clean'. The original Where No Man Has Gone Before soundtrack release had Force Field and Silver Orbs (Season 1, Disc 1, Track 20) as their original separate tracks (which, for instance, meant we could hear the full end of Force Field, as in The Lights of Zetar teaser). I also suspect the Starship Party cue in Is There In Truth No Beauty? (the last cue in Season 3, Disc 4, Track 2) was probably recorded as 'clean', because it's used 'clean' in several Enterprise orbit shots in other season three episodes such as The Mark Of Gideon, whereas in the set it is merged with the previous I Must Know cue as in the episode. In some ways, the set does present the 'edited' cues as opposed to totally 'clean' ones, since even in their intended episodes, merging and adjusting went on, and the set seems to follow this through for a few cues. My theory on the latter cue is speculation, of course, since the original ITITNB music has not been released before now.