I love the backstory of this era, so I hope you don't mind if I chime in even if that isn't what prompted your supposition.
In-universe, it certainly looked that way. However, in real life, Eric Kripke had to be pragmatic. While the oft-repeated story about his five-season mythic arc is true, that target sat on the more optimistic end of the spectrum. Initially, he had to dial down his expectations and adjust as the show went along. He originally targeted a three-year arc, which was the industry norm back then; Jeremy Carver was later quoted as having the same target.
Wikipedia and The Futon Critic
Meanwhile, Sera Gamble operated on a two-year plan based on her contract. Andrew Dabb was the lucky one who didn't have to worry about cancellation. By Season 9, CW President Mark Pedowitz stated that Supernatural was virtually guaranteed a renewal as long as viewership stayed steady—and it did, consistently remaining in the network's top three.
From my understanding of the TV industry, when a new season premieres, a show typically has 12 or 13 episodes pitched to the studio, fully plotted, and ready to be filmed as production kicks off. If the network gives a "full-season order," the back half of the episodes goes through the same approval process later on. For Season 3, the 2007–2008 writers' strike disrupted that back-half order. They only had up to episode 12 locked in, which was originally supposed to be "Mystery Spot" before the episode order was switched (more on this below). "Ghostfacers," meanwhile, was written after the strike ended.
When the strike hit, Kripke pivoted. In my opinion, the tentpoles of the story stayed the same, but the pacing of the myth arc was stretched and padded. The core concept of Sam going dark to save Dean was always there, except the original plan was to save Dean before he went to Hell. Because Dean wasn't dragged downstairs in the original draft, the concept of breaking the 66 seals didn't exist yet. The strike robbed them of the narrative momentum needed to show Sam successfully saving his brother, so Kripke abandoned that route and let Dean go to Hell.
This pivot directly birthed Season 4's angel mythology and the Michael vs. Lucifer conflict. While Sam being Lucifer's vessel was always part of the master plan, the original endgame was simply brother vs. brother, with Dean forced to hunt down and kill a corrupted Sam.
Regarding the episode switch: "Jus in Bello" was originally meant to be episode 11, followed by "Mystery Spot." When the strike made the future uncertain, Kripke flipped the order so the show could end the strike-shortened season run on a high note. Personally, I love this change. The continuity works beautifully: seeing Dean die countless times in "Mystery Spot" leaves Sam hardened and callous. This directly feeds into his darker mindset in "Jus in Bello," where he focuses entirely on the big picture and is willing to sacrifice Nancy Fitzgerald to save the group.
tldr; So, to answer your question and hypothesis: yes, Ruby always intended to help Sam, but her goal was to lure him to the dark side so he could become Lucifer's vessel based on the first 12 episodes. The complex plotline of breaking the seals was simply added to the narrative later—briefly teased when Dean went to hell in the season finale. Ultimately, this works retroactively as both angels and demons wait with bated breath and with excitement for Dean to break the first seal in hell.
P/S: On your rewatch, pay attention to episode 3.05 Bedtime Stories and 3.09 Malleus Maleficarum. Tammy, the demon witch, said the demon gunning for Sam was a "he." Eric retconned and changed the new leader to Lilith in 3.12 Jus in Bello, quoted in the above Collider article: "We just knew that there was a higher demon. And then, we decided to make her a woman because the first demon was a man. So, these things evolved."
In 3.09, Tammy said, "There's a new leader rising in the west, and he wants you dead."
Also in 3.05, the crossroad demon said to Sam, "I'm just a saleswoman. I got a boss like everybody... he holds the contract."
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