Energy isn't conserved in general relativity, particularly in an expanding universe. So if you try to reason than x must be true becasue otherwise energy wouldn't be conserved then you could go down a road of thinking many incorrect things. So don't do it.
Intuition 1: The growth of the scale factor can't exert a force on anything
Forces are not exerted by gravity, gravity isn't a force. Forces are exerted by pressure and stress. But we can't conclude there is no energy. Dust has non stress and no forces, but it has a nonzero energy density. And it has different amounts of energy density in different frames. Just assuming something doesn't have an energy would be wrong.
Intuition 2: The growth of the scale factor increases the relative distances of things over time, which is the same as giving them a relative velocity.
You do realize that velocity is relative to a frame? If you frame is to comoving frame of the cosmological fluid then everything is at rest in that frame if the peculiar velocity is zero. Being at rest relative to your frame right there is a real thing. Having your distance compared to something else somewhere else isn't even physics. Physics is local.
Relative velocity is the only kind of velocity, so this motion ought to have an associated kinetic energy.
It's not motion. Motion is relative to a frame. It's just breaking a tangent of a worldline into frame dependent parts. There was a worldline, it had a tangent. That was real. And then if you pick a frame you can brake that one tangent vector into parts, if you wanted to for some reason. Like if you hate energy-momentum and want energy and momentum instead.
This should in turn contribute to the universe's energy density, and thus the growth of the scale factor.
The energy density does change. But not because there is zero velocity in the comoving frame.
Intuition 2 seems stronger to me, but I don't see how it's compatible with conservation of energy.
Both intuitions are wrong. But there isn't conservation of energy.
I've not seen any contribution from this supposed kinetic energy in Friedmann equations
Because there isn't kinetic energy in the comoving frame from a zero velocity in the comoving frame. Physics is local.