OK, sounds some what reasonable. But flipping points might turn out to be to harsh on attackers aswell:
The painfield (I guess you guys are working on those to get reintroduced) will cripple or kill many attackers if flipped.
With NPE in mind you probably don't want to do this because it's not as wide as AMPs and the spawns can easily be camped. Halve of Esmair fights take place in/around biolabs and I know for sure I won't go there if my faction only owns one spawn and the enemy has three (as an attacker), because owning the sidespawns also means you can suppress the attackers way better due to shorter distances to the spawns AND pads.
I'll stay at my proposed defenders penalty. Maybe even 20 sec, because:
If you manage to loose the SCU you should be at a severe disadvantage, but it could give an organized force enough time to team up and do some damage.
Timers depending on ownership of the base should be possible right?
...