For that i think locking down that middle bottom area (the medium height) will direct them to the good place. Still, the early enemy combat will probably remain an issue there. but at least they will be guided in a good way.
To solve that issue i think looking at how doomsday was made is going to provide alot of help. Although you can go straight to the enemy spawn it still gives you a better focus on the 2 objectives: A cp and a flag.
In your case the whole flag area is gone gameplay wise and focusses them to go to 1 side. Thats what i think going to give a big issues because they have combat very early. Something like the raised middle area in doomsday should be done. I did draw the idea i have to at least give it a bit more a doomsday like playstyle and delay the early enemy combat from the merged paths.
See the image for what i mean with a more doomsday like area:
It doesnt have to be the solution, its just an idea.
Note, the tunnel is only needed if you WANT the early battle, if you dont want it dont add it.