But as far as gameplay goes, it's not exactly encouraging or fun.
i think that really depends entirely on whether you have means to fend it off. if you had a million credits, your fleet seems quite small for that. also, now that you know enemy fleets striking at your colonies is a thing, you can prepare for next time by starting to build an orbital defense station, which can make a huge difference in battle.
I think the bigger point is how the transition goes. I agree with Alex that Colonies fill the spot of the 'end-game' of Starsector, but it just seems like it's relatively /easy/ to set-up a colony now when you're entirely not in a position to maintain it, let alone defend it. There's also the issue with no 'small' expeditions/Raids (balanced for the 'risk' you pose), the first basic one even from Pirates being relatively a mid-late game fleet. There's also the matter of how colonies as they are now, optimal gameplay dictates that it's not only counter-productive, but anti-play to 'live'/grow alongside your colonies, and when you do plop one down, within two months it should be entirely maxed out, having thrown a good million or so at it, and 20 hours of exploration loot before hand at it.
It's just easy, middling around in Starsector, to end up in that position where you can do something and it's fun and it's new gameplay oppourtunities, but you don't take them because the game is 'rigged' to punish you. Not designed per se mind you, just for the moment, it seems like a red-herring proposition.
And yes, you can abandon colonies and yes, there is room to make mistakes and come back from them, colony-wise, but it's also equally easy to invest a lot into them, and end up fleet-less, colony-less, -200k in the hole, -repped with everyone and basically in a situation where starting a new save would probably be smarter.