You can, but there are two very important things that need to be known if you want them to initiate a counterattack:
1) Arcann and Thexan's fleet would have successfully destroyed the Martian forces if the two had led the attack on the planet. This is because the two are incredibly overpowered, while their fleet and initial strike force were not up to the task of overwhelming and defeating the Martians despite being able to decimate Earth, Korriban, and Tython respectively.
2) The Zakuul strike force that attacked each planet is NOT a representation of the Zakuul fleet entirely. Without spoiling too many details, the true fleet of Zakuul is capable of decimating the entire multiverse at Valkorian's choosing. Meaning that if you send the Martians to fight against the Zakuul fleet, you'll need to prepare for them to get utterly crushed for reasons that will be explained if/when we reach that point in the story.
Also, one more thing. The situation between Vegetto and Brachi is definitely something I want to keep playing out realistically, but when the time comes, she will need to rejoin the main cast by the time they confront Valkorian in order to stay as a main character. If you don't believe she will logically rejoin them by that point, then I can downgrade her from a main to a regular casted character in the story. Keep in mind though that a MASSIVE character change will occur for any characters that aren't mains due to a point in the story that won't be counterable, so if you want to RP her the same as we've been doing, then keep her as a main!
It's entirely up to you, since I believe either course of action actually would be a fun RP opportunity for you.