Helping the runner

[BigGref]

I was wondering how many people, or better yet how often to most people call the helping the runner penalty (at what level, when, etc.). Reason asking is because Friday my WH threw the flag for the penalty (after looking at the tape it clearly fits the definition and the Offense gained an illegal advantage {be it only a small one}) I wouldn't have much problem with it but it was a 2nd half, team thats down by 1 TD, around opp 30 yl, 4th and 1 and the contact was after about 2 yds of gain (so the illegal contact really had no influence on the BIG PICTURE of the play). So would you let this go in this situation with above variables or would you go by the letter of the rule, or warn offender, or maybe call it easier at different time of game? thanks!