As of yet though, there are tricks for it:
a] if you haven't developed your fleet capacity to maximum, you can start another upgrade, then select your units you want to build, then cancel the upgrade. As soon as your negative fllet point counter zeroes (i.e. you lose or scuttle enough ships), your queued ships will start building and the RA will not interrupt that.
b] Select a group of any number of the same unit, Pause the game, press scuttle -> tab -> scuttle -> tab -> .. and so on with every ship in the group.
Unpause the game and after x seconds you will have a large amount of fleet points freed at once. Pause the game immediately, queue what you want, unpause.
And it is good the RA was changed. It is still good very good, but not as game-changing as it was before.
In 1.05 the game looks like this:
no RA -> manage your empire to have resources to build units to conquer and have more empire to manage
with RA -> move your always-full fleet to where it can do most damage, spend money on planet upgrades and Pirate bounties
. Don't bother withdrawing - the more damage you do now, the lesser resistance you will have to face when you rebuild your 2000 unit fleet (which is less than 3 minutes later, cause your ships are already ready
)