Yes, you can train a pomegranate tree to stand upright with a single trunk. It takes a lot of attention, but its doable --- I've done it.
Pomegranates tend to sucker heavily from the base. You need to repeatedly cut those suckers off or you''ll quickly have a multi-trunk tree. I clean my tree up at least 3 or 4 times a year.
They get top heavy and flop over, even without fruit. You'll need to stake it and continually pull it back to vertical. If a stake isn't enough to keep it upright, then attach ropes and yank it back to vertical.
Prune the fruit AGGRESSIVELY. I remove all but one bloom, and that fruit is close to the trunk, not the end of the branches. If you don't, the heavy fruit will pull the branches down and the tree will tilt toward the heaviest side. I thin the blossoms by aggressively cutting back the branches to leave only one blossom (or one blossom cluster, of which I thin away all but one blossom). I continue to do this all summer because the tree will continue to flower for months.
In the winter, get a step ladder and thin out the center branches of the tree. Leave the main scaffolding branches, but open up the heart of the tree. I have one central vertical trunk that goes up about 15' or so, and then about a dozen main branches that come off of it. It's taken years to get this structure, and every year when I'm up there thinning the tree out again, I question, "Is this worth it?" But now that the fruit is huge and ripening and accessible, I remind myself again that all that hard work of thinning the tree and thinning the fruit is worth it. Long, leggy "water shoots" tend to shoot up and then flop over once they are a couple of feet tall. You've got to decide what to keep and what to remove, or just what to shorten. Again, it's an ongoing process. After 10 years or so, you won't have to be so aggressive, but initially when you are forming the primary tree structure, it's an ongoing battle.
One other benefit of training your pomegranate to grow with a central trunk rather than multi-stem is that it makes dealing with ants so much easier. If you keep the branches from dropping down onto something else (like a fence or another tree where it creates a bridge for the ants) and you keep the tree to only a single upright trunk, then you just put a band of tanglefoot around the trunk and it keeps the ants from the fruit.
If that were my baby pomegranate tree, I'd transplant it to a bigger pot, stake that little shoot upright with a 4 foot stake, and begin training it to be the primary trunk. In two years, it'll be ready to go into the ground. Pick any fruit off of it for the first couple of years—there will be plenty to go around in 3 years or so. Pomegranates grow really fast. Focus on tree structure and keeping it vertical and straight. They are squirrelly trees --- make it mind! In the end, you'll be glad you put in all that effort.