While Knowles does make it clear that Gene has accepted responsibility for what happened to Finny and that life would never be the same for him or the surviving Devon boys without Finny and because of the war, I do not believe that he implies that Gene "put the experience behind him." After all, the novel is told in flashback because Gene as an older adult returns to Devon School to walk the grounds and visit his and Finny's old haunts.
In regards to Gene accepting what happened, on the last page of the novel, he reflects:
"I never killed anybody and I never developed an intense level of hatred for the enemy [during WWII]. Because my war ended before I ever put on a uniform; I was on active duty all my time at school; I killed my enemy there" (204).
Gene does not mean that he killed Finny as his enemy, but rather that he fought and defeated the insecure part of himself that caused such jealously toward Finny. He finally found a "separate peace" within himself.