This isn't an exploit. We are all aware of this, even in GC1. In effect, you are gassing those colonists into space...

Keep in mind, the reason morale is rising is because the population is decreasing which also means less tax-payers. Best way to keep moral at 70% and above is to either not upgrade farms, or build appropriate entertainment centers.

You're increasing your approval but lowering your income. Plus you're spending all of that money on the ships to kill your people. I don't think it's too exploitative. Cruel, perhaps. But not game-breaking.

No better way to kill morale than to research farm upgrades. The morale penalty for population seems extreme. In my first game of reasonable length, I made the mistake of building a farm on a 300% food bonus tile. Even with Populists and 4 Arenas on the planet, I couldn't manage more than 40-50% approval on that planet, while other planets with a single farm and no upgrades had approval ratings of 85-100%.

In GC1 you could ship out 50% of your population. Now that could be called an exploit. I have never noticed that much effect from shipping out 500K souls at a time but I guess if you pumped them out fast enough it would make a difference

I just load transports and don't kill them. If I don't plan to invade anybody anytime soon, I simply swap out a couple engines for an extra troop module. I have never had a problem with too many transports; it's nice to be able to immediately populate a new planet with 2 billion people. And, of course, two words: Traditional Warfare. If the morale problem's happening before I've researched Planetary Invasion, no big deal--I probably haven't researched Interstellar Republic yet, either.

Another solution to morale is simply to let one or two planets sink to 39% and stop growing. It's really no big deal; it's your overall approval rating that matters. Also, if you get a 300% food tile (and you intend to farm it at all, which I do), build a Basic Farm on it, before you get Xeno Farms. You can wait & see what happens later.

As far as I've seen you want 1.25 - 1.5 morale increasers for every farm.

Build 2 farms, build 3 morale.

On a 300% farm building you essentially build 4 farms on the same location
Which means you need almost 6 morale. If the morale buildings aren't equal to the farms in technology level.. you need more of them.

I tried having some transports in space, to control my population, but then the AI got nasty. Use colony ships instead if you wanna do this.

What's the point of colony ships? A few of them, okay, you can ferry population & populate newly-taken worlds. But a lot of them...???

It'd actually be rather nice if decommissioning colony ships did something to your alignment, as you are effectively spacing those colonists.

On a 300% farm building you essentially build 4 farms on the same location Which means you need almost 6 morale

Morale penalties due to population are capped at -80, which occurs at around 24 billion population. Anything above that will not affect morale any further. In my experience you never need to build more than 3 or 4 entertainment buildings (depending on which trade goods you have, number of mined morale resources etc).