Crew members' influence on The Office

There are a number of possible reasons.

1. The Jim/Roy fight was between two men while the attack against Pam was a man attacking a woman.
2. Dwight was already quick to intervene in the Jim/Roy fight, in fact there is quite a bit of emphasis on Dwight's quick acting heroism.
3. Its possible the boom mic guy didn't even work on the set for the first fight as it happened years earlier. (Update: after rewatching, they do mention that he has been working on the show since the beginning so this point is invalid)
4. As evidenced at the end of the series, the crew was quite emotionally invested in the characters by the end of the show but were probably not as invested in Season 3.
   
   EDIT:
5. Brian's character plays an important role in the story of Jim and Pam drifting apart in the final season.
6. This is the first time in the series that anyone in the film crew breaks the 4th wall and Brian gets in trouble for it the first time when he comforts Pam and then gets fired for intervening. They were under strict orders NOT to intervene.

The other important point the other answer missed is that Pam was alone in the parking lot when Frank charged towards her. Only the crew (Cameraman & boom mic guy) were there. So naturally, Mike intervened & saved Pam.

When Roy attacked Jim, there were other people around to intervene so the crew could let the confrontation play. But if they let Frank attack Pam while they film it, it would be pretty shameful & inhumane on their part