The reality is that we don't really know, because of the funky way the game played out.
I think it's clear that the patriots wanted a ball-control offense to limit the Jags possessions, which is kind of ironic, because all the prognosticators sort of suggested it would be the opposite. So in that sense, I think the deep ball was not really something they wanted -- even if it's complete it tends to put the defense back out on the field more quickly. Patriots were taking the full 40 seconds on every play, and you could tell everyone understood they were to stay in bounds and keep it moving.
On offense, look at the yardage the team had to go on third down: 2, 1, 2, 14, 3, 4, 1. The 14 was on the drive at the end of the second half where clearly the team was trying to leave Jacksonville with as little time as possible on the clock and just trying to get in field goal range. The play call there was a short dump to Welker.
Anyway, as to whether Moss was in the game plan, I have no doubt the patriots would have thrown to him if it had been the higher percentage play on any play, but it just wasn't except once. The Jags never changed their approach, and the patriots took what they were given.
The reality is that I think the Jags made the right choice. The problem with a dink and dunk offense is that one offensive penalty -- a hold, an offensive PI, or even a false start, often derails you. Patriots offense only got flagged once, I believe, so it didn't work for the Jags.