There are little red flags that are going up here.
For one, as was already mentioned, he was the only real spiritual mentor in her life, and especially, he was an official pastor to her, which really kind of makes things rather edgy. Here in Canada, it IS actually a legal matter... sexual misconduct. But even beyond the legalities of it, as I know not every country has the same legal stuff, there still is a power/authority imbalance here, which will have VERY wonky dynamics further down the road, if they are not already wonky.
Second, there is the timing of the whole thing. This girl was currently with someone else when they started dating. Even if there were misunderstandings and he thought they were broken up for 2 weeks... consider this: is 2 weeks long enough of a break between such serious relationships? I would think not. And especially if this guy was not 100% certain that this was the truth (which apparently, it wasn't). Breakups take a while to heal, and I hesitate to advise anyone to pursue that kind of relationship with ANYONE so close to a breakup, especially if the person I am advising is the one just broken up.
And I don't think that 5 months absense is a long enough time before even considering dating. If he was gone for a year or more and she had more time to develop spiritually, without his influence, then this part of it may not be as much of an issue.
Third, I am grieved by the church's reaction to this. You say that they rebuked you and told you to not hinder love, and to not keep love in a box? That's funny, because what is happening here is no more love than the "Love" that is proclaimed by the media, which is really just hormones, lust and sexual attraction. For one, this girl lied and this relationship started in deception. True love means standing up for the truth and for the best interests of the one who you love. It does not mean sitting silently as one of your own is stumbling in sin because you don't want to sound "judgmental"... I can see by the ministry with youth at your church that you are not in a position to leave right now. But you can still say something, even to the senior pastor, who can address it in a more public and official manner.
The age question, I am not really too sure about. Some say it is just a number, especially after a certain age, but what is that age, and what are the limits? I have a friend who is 25 who is interested in a girl who is 18 (but turning 19 in December), which would be a 6 1/2 year difference, and I have no clue as to what to tell this guy because I really don't know. In the case of the OP, though, the fact that their relationship most likely started when she was younger, (though not officially) is what makes me begin to question, because dating minors is a legal issue, as well as a sketchy moral one, namely pedophilia.