[X] Save the yeerks instead. They have useful abilities if you can get any of them to work with you, and failing that you might be able to sell them back to their empire for a cash ransom or diplomatic considerations.
[X] Go with the original plan and visit the armory, letting Jonathan work his magic and conceal a bunch of weapons. They expect to get some electrorifles, net guns, and maybe other stuff. The yeerks seem evil enough that you won't shed any tears over losing them to whatever fate the government has in store.