The Geth are different after the upgrade. Tali tried to explain the Geth in ME1, and eventually just went with something like "they're incredibly complex, and have been changed/upgraded themselves for 300 years." Because they are constantly shifting hardware platforms, they have no fixed personality, or no personality. The only reason Legion has a personality is the extended mission in ME2 that it was on where its runtimes existed on one platform for so long. I don't know if they would judge the difference from the upgrade the same way we do.
To me, the Geth after the Reaper upgrades are updated s\w running on the same hardware, memories, experience, and history as the previous Geth. Gone? Probably. Old Geth changed and therefore gone - I'm not sure they would judge it in those terms.
It isn't so much that they upgraded themselves its the insane degree for which the upgrade changes them. The Geth were essentially VI processes that linked together to form the equivalent to AI. They are not technically AI in the same sense that we consider most AI to be AI. They do not value independence but rather unity. The reaper upgrade destroys this and makes them each an independent AI. They no longer rely on the connectivity with multiple geth programs to form one complex entity. Before it was "there is no individual" but now thats completely changed. The geth, imo, are one of the most interesting forms of AI I've ever seen in fiction and that comes largely from how nontraditional they are.
To quote the Wiki:
"According to Legion, each geth is made up of hundreds of programs equivalent to VIs, all operating in parallel with one another to form a kind of emergent intelligence"
Individually the geth are no smarter than a varren. It is only through unity and connection with other geth do they gain complexity and intelligence. The reaper upgrade completely changes this. This is like jumping from Linux to Windows. It isn't so much a upgrade as it is an entirely different OS. I get that the geth likely don't view the upgrade the same way I do, and they might be right. I'm only saying that from my perspective all my interaction and experience with the geth feels like it was with an entirely different species to what they are now.
Legion even seemed like an entirely different 'person'. The geth's perspective on accepting the reaper upgrades are drastically different between 2 and 3. So much so that its like they're written by completely different writers. Which apparently they were.
I suppose it's easier to say such things if your species is not on the edge of extinction. Without the reaper code the geth simply have no future they could build. If they hadn't used the upgrade it's unlikely that Shepard would have been able to convince the quarians to stop the attack. Shepard used the upgrade as leverage to convince the quarians that they would be wiped out if they continue the attack. So I don't hold it against Legion for using the upgrades on their own terms. And "sticking to your principles whatever the cost is" is one concept the Geth logically wouldn't share.
I would argue that 'sticking to the principles' is a concept the Geth share. The entire reason the heretics split up from the geth was because of a difference in principle. Also Legion could had just lied and said it was giving the code to the geth. It isn't like the quarians can tell what geth have the upgrade and what geth don't. They'd be completely oblivious to it and have to accept Shepard's word - something they potentially do anyway without any proof to back up the claim.
I hold "using the upgrades on their own terms" against Legion because it is DIRECTLY contradictory to the geth in the second game.
"Legion believes that the technology in the Collector base should not be used, for humanity has the potential to create their own future without it.
If Shepard chooses to destroy the Collector base, Legion calls it an interesting choice, saying humanity was offered everything geth aspire to - unity, understanding and transcendence. Legion adds that Shepard even rejected using the Reapers' technology to achieve victory on humanity's own terms, and comments that the Commander is more like the geth than Legion initially thought."