If you don't want colonies to be attacked and don't want space battle to be a thing either, simply add "resource nodes ( planets ) " which give all commonwealth in the federation a boost to a specific resource production when captured. These nodes can be defended and attacked.
Military units ( biological and mechanical ) should however be created on colonies and launched on a ship to attack a node or to help defend it. We would have buildings that converts population or robots to military units.
Ships would be created like rovers but use military units to create and move around just like rovers. To launch a ship we need to send them through a building called a Ship Warp Gate.
To get rid of the space battle rendering part, simply add a "star chart" building to list all nodes as simple text details and text details of the progress of the war ( ship ETA, enemy unit type etc ) .
Units need to be balanced though, with relative weaknesses and strengths.
To balance the "1 Fed ruling the entire galaxy", and Feds dedicating 1 colony to military production, simply limit the ships that can be sent per hour per every member and use that feature you already have to create distances between colonies and nodes, the closer the node, the faster reinforcements can reach it and the less oil needed to ship units. Maybe add different ship types and only smaller ships can travel further distance?
If you actually manage to balance units and they fight like real wars, they should last a few real time days to maintain intensity ( ie. server sided like GTB ) based on army size with only a few hundred units dying a minute ( about 1 million a day ). When a node is captured it will become an eternal struggle to defend it, continuously trying to counter your enemy units, making far away nodes difficult to hold.
Tbh, war efforts is a good way to balance endgame resource accumulation, and if you look at it this way, the fighting is so that we can generate more resources :D.
Just remember Dev, competition causes the player base to grow and helps sustain the game with an active player base.
When it comes to end game content, this is the best suggestion I can give that doesn't affect new players at all and allows those base builder people to feel happy and safe because it doesn't affect them.