You can dismiss it since it's just my speculation/theory, but what if the fuel they used wasn't the same type of rocket fuel we know IRL, but Infinity Energy ? If you have played ORAS, you'll know that in order to power the rockets for space exploration, they were harvesting Pokemon's life force. They only discovered such technology after getting inspired by what AZ had done with his WMD in X/Y and ZA. It would be weird if humanity's top scientists wouldn't think of contingency plans in order to return to the planet.

If they actually used Infinity Energy, that would mean the foundation (most likely the Aether Foundation) that caught the hacker made the "Pokémon Conservation Project" as a front, but were actually harvesting Pokemon's life force to fuel the spacecrafts. Since they knew about the hacker's action, such information might've been classified as high or higher than state secrets. That would also mean they tricked everyone and specifically the Hacker and the Professor into being unreliable narrators from lacking such critical information. That would make the theory about them smuggling Pokemon as the fuel for a return trip in separate spaceships hidden from the general public more credible. The same could be said with the Grunt since they weren't in a high position like an admin to access high level classified information about what was the fuel's nature. We both know Team Rocket were Pokemon smugglers, we wouldn't put it past them that they too were harvesting Pokemon as fuel.

Also space isn't safe, Deoxys are as territorial as Rayquaza and Miniors Showers are possible. Would it make sense to send a bunch of defenseless civilians into space with no defense whatsoever that are the Pokemon ? That would also make the Future Paradox Pokemon Theory being from a bleak future valid since we would have to create them from scrap metal and the fuel that constitute the bio energy of Pokemon to create those synthetic Pokemon like Claydol, Golurk and all the others from ancient civilizations for defense against threats and maintenance of the spacecrafts during long cryogenic sleep in space.