Killing the Geth isn't self-determination, but neither is wiping out the Batarian star system in Arrival. ME, as a series, has a lot of themes. Hard choices is one of them, too.
Each ending has its merits, but I do think the destroy ending is the one my (paragon) Shepard is most likely to choose. Because (from the character's perspective -- they don't know everything the player does):
- Merging with the crucible is bound to change me. I could barely control myself just moments ago around the IM. What if, after 50k years, I start thinking like this kid too?
- Combining organics and synthetics? What does that look like? How do people change? Are we talking about fresh evolution? Legion had a point when he said such things should not be handed to people.
- Killing the Reapers has a predictable outcome. The Reapers are gone, the relays are gone, and the galaxy has to cope.
- Geth and EDI are horrible side effects I will have to live with, but the galaxy is bigger than them.
Given the choice, she'd kill the reapers without killing the Geth and EDI, but since that's not an option, just pile on more guilt!
As a player, it is pretty obvious that synthesis is the best outcome. At least, it was portrayed as such to us, never know what the actual consequences are. But, I spent a ton of time thinking about it and came to the conclusion that destruction is the only logical choice for my Shepard.