Well, the central point of both campaigns was the fact that the blight was spreading so fast that much of the planet's resources were effectively inacessible (already over-run or couldn't safely be harvested before being over-run by the blight). If there were enough resources for two starships then why waste time and precious resources building weapons? The simple truth is that only one side made it out, taking the children of the the losing colony with them for humanitarian reasons.
In all likelyhood Eden would have been the ones to escape as they were more advanced technologically. The RLV allowed them to save their resources for the starship instead of having to waste it on one shot rockets.
Even if we assume both side managed to build a starship, Eden's would stand a better chance of success on arrival at a new planet. The RLV would allow them to pack every last scrap of metal they had for the voyage for use on the new planet.
As for the whole "who's the bad guy?" issue, it should be remembered that eden didn't intend to release the blight, it escaped. The bug had been created to terraform the planet, so presumably they would have designed it so that it couldn't get into their buildings/vehicles/spacesuits. How the BLight gained this ability is unclear (it could have been intended as a bioweapon designed to only infect a small area, but its more likely that it was unintentional, it amy even have evolved that way after its release!). In any case it's clear from the storyline that everyone involved in the development of the Blight was killed in the explosion of the lab (a meeting on the situation was being held in the lab at the time). This means that whatever the sins of Pre-Blight Eden might have been, the Eden in the game wasn't responible for them since they were those who were involved in the upkeep of the colony.
Edit to add: Since in both stories Axen Moon stay behind its possible that (as Nightmare said) that he lead with Plymouth to build a second starship. A sencond starship would likely take fewer resources to build since they would have the lessions Eden had learned from their effort (once the RLV launches the tech in Eden would be free for the taking (if we assume the colony is destroyed shortly after the launch of the RLV we can suppose that Axen to the computer files with him). The resources needed would also be less because it wouldn't be necessary to do any prototyping. Plymouth would also have the design for the RLV further lower the resources needed. They could even us their newly aquired RLV to fly to the last area of the planet to be infected and thus save on having to build a new colony everytime the Blight gets close. This "sub-orbital hopping" could even be used to access resources that would otherwise be inaccessible (i.e. those for which there is time to set up a mining base but enough time the get back to the main colony before being overrun by the Blight). They would also have been able to salvage Eden's skydock for resources.
I think its quite possible for the surviving colony to have scrapped together enough to build a second starship or at least an interplanetary ship (New Terra shouldn't have been the only planet in the system after all). If they managed to reach another planet in the same system they would have all the time and resources they needed to build a new starship.
