In terms of a hypothetical original ending, there are a lot of possibilities. Maybe the showrunners wanted something which would have taken a much higher budget to pull off. Maybe they originally planned to extend the Klingon War into the second season a bit (e.g, they hadn't figured out how to circle the square yet) and CBS came on them like a ton of bricks. Maybe their planned ending either openly broke canon, or was vetoed as too grimdark. The one thing we do know is the last 1-2 episodes were not filmed yet when the pilot aired, meaning it was the first time that CBS got real outside feedback on the series - feedback which could have changed their plans. Particularly because the "new Klingons" were the most heavily panned element of the pilot, and the idea of extending Klingon-heavy content into Season 2 might have freaked CBS out.
I agree there were structural issues with the show all the way through, most of which boiled down to writing. But they didn't have the weirdly slapdash, perfunctory feeling the end of the season finale had. Basically the whole "rah rah Starfleet bland optimism about the human condition" came out of nowhere. Then they set up the final scene to essentially say "okay, we admit that was all shit - just forget about it - but look, here's the Enterprise!" It really looked like to me someone had sat Berg/Harberts down and told them they had made a total mess of the season, and demanded they do a 180 and start the second season with an almost clean slate.
Maybe I'm too cynical, but I thought the "rah-rah Starfleet" speech was pre-ordained from the very beginning, and the writing of it didn't strike me as much more heavy-handed than a lot of what the show served up previously, such as the Sudden Tears for the Tardigrade. I complained about the use of narrative shortcuts all season, so I can't say I was shocked when they used them in the finale.
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