I just saw the movie for the first time yesterday, and I can see where it might give the impression of having a pro-Soviet slant, but only because it's a somewhat dumbed-down adaptation of a much more complex novel.
The film exaggerates General Midwinter's rabid anti-communism to cartoon proportions, and adds a ludicrous invasion sequence to give the story a big cinematic climax (quick question: did "Harry Palmer" really walk all the way back to Helsinki from the middle of a frozen Gulf of Finland..?)
In Deighton's book the conflict isn't between Communists and Capitalists: it's between professionals and amateurs. Palmer and Colonel Stok, despite being ideological adversaries, were both professionals and shared a common bond of professional knowledge and experience.
Here's Deighton's protagonist (nameless in the book, and better that way) speaking to his one-time friend and misguided foe Harvey Newbegin, in Leningrad:
"Listen, Harvey. Just because you've been playing electronic monopoly out there in Texas for too long, don't get the idea that you're in the intelligence business. Every senior-grade Russian intelligence man knows that I came into town on the train last night. They know who I am just as I know who they are. No one puts on false hairpieces and pebbles in one shoe and sketches the fortifications anymore."
Regarding your other point: I wouldn't expect a Russian like Stok to admit that his country was "occupying" Latvia during the Cold War. Once again, the original novel gives that scene a deeper political and historical perspective, all but lost in the superficial screen version.
"Sacred cows make the best hamburger." Mark Twain