You can certainly cut off the long trunk. The smaller ones down lower will just start growing once the main trunk is gone.
Bonsai is a waiting game. You can't make an instant bonsai unless you have the material already grown. When you start off with a young stick you can only make a young stick bonsai or you can leave it to grow for a few years until there is enough branches and trunk to make a realistic bonsai.
Juniper procumbens is a natural ground cover so the main branches will always try to grow out horizontal as it is now. That does not mean you have to leave it that way. In bonsai we manipulate growth to achieve the shapes we want. If you want a more upright trunk just wire that long branch and bend it into a more vertical position. After a few months it will stay that way. Thousands of these are produced every year by winding the main trunk round a stick at the nursery resulting in the abominable S shaped procumbens pre bonsai. The problem with that is there is little taper in the trunk so they still look very young. It takes quite a few years for the trunks to thicken and look really impressive. If you decide to wire the trunk upward try to avoid the lazy S shape. Try for some sharper bends and some a little closer together to get a random look for the new trunk.
So much depends on what you want to achieve with this tree.
If you are happy with a small green pompom you should chop the long branch off now.
If you would be happy with a taller, skinny upright juniper you should wire the trunk appropriately.
If you want an impressive juniper bonsai you should plant this one in a large pot or in the garden and just feed and water it for 5-10 years then reconsider the bonsai potential. Or you could invest in some more mature stock that has enough size and character to produce a more immediate bonsai.
