The idea that Ruby was supposed to be the companion for both seasons really does make far too much sense when you look back on the second season. One issue I did have with Belinda is that she did seem to take a liking to the Doctor way too quickly for someone abruptly removed from her day to day life (and now we know, a daughter) and seemed surprisingly tolerant of the fact they had to jump around to different time periods to use the vindicator in order to return to May 2025. Now if it were Ruby, that would be easier to accept, given her pre-existing relationship with the Doctor. Sure, she's annoyed at the disruption to her routine, but given she knows the Doctor she could quickly fall back into the rhythm of their friendship.
The one hiccup with the theory is if Ruby were the S2 companion, who would Lucky Day have been about instead? The only other possibility I can think of is Rose Noble, and instead of Ruby's PTSD making her believe there are aliens everywhere, it becomes Rose's enthusiasm and desire for adventure making her believe there are aliens involved. Problem is, given how much of a piece of shit Conrad was, I can't imagine wanting to fake a relationship with Rose, even with the intent of using her to discredit UNIT.