A large amount of the augmentations the Gravemind made to High Charity was to generate neural physics and keep the superstructure intact. When he detected the portal nearby Mars, he was probably freaking the hell out and didn't want to waste any time with the array possibly being activated at literally any time. (It could have already been activated for all he knew). So he decided to head to the Ark from there. As for not destroying 04b, there was nothing he could really do about it. as soon as High Charity entered the Arks's atmosphere, it began to shake itself to pieces. We see this with all the derbies in the cutscene raining down.