I had a similar problem, we had 2 male gerbils who lived together in peace for nearly 1 1/2 years. Then one day, one of the boys escaped, and was out of his cage for about 18 hours. We found him, but when he was reintroduced to his cage mate, a furious, and bloody fight broke out. No matter what we did they would attack each other.
We tried something called a split cage, where there was chicken wire dividing the cage in half, and we would let each gerbil spend a day on one side, then switch and go to the other side. After about a week the two boys were ok.
I've used the 'split cage' several times since, on gerbils that were complete strangers. It can take some time, up to 14 days but it has always worked.
Gerbils do indeed fare better together, but if your little guys are violently fighting I would say that an execption should be made as you don't want them to kill each other, which, unfortunatly can happen.
Good luck,
Louise