I happen to agree with Lukkai.
Her past experiences back at the lab/school/home for pedophiliac suits was a horrible thing she did not want to think about any more than she had to. Killing Hooper would have caused them to go looking for whoever did it. Further, while hunting Hooper, it would increase the chances of the Center finding her (by them discovering someone was being nosy and tracing the efforts back.
Then there's the fact it would also force her to confront the memories. Many people suffering from traumatic experiences tend to wind up with avoidant behaviors. They will do whatever they can to avoid anything that might remind them. Trust me, I know whereof I speak. So for her, all she wanted was to forget all about the Center (never happen) and hope they forgot all about her (might happen).
As for the arms sales, you have to consider Jordan's brain. The risk to her becoming caught by selling these weapons came less from the Center than from the more usual authorities. Unless the Center was so utterly convinced she was alive AND an arms dealer they wouldn't really have any reason to be tapping into the Hague. So being sent back there after being caught really wasn't a significant risk. On the other hand, it was an amusing challenge. Jordan doesn't give a rats ass about human life in the general. (Specific human lives, yes. Just not the generic ones.) So for her there is no moral compunction to avoid arms dealing. It was, however, a relatively high risk activity with a high return on investment. So it was somewhat challenging. A mind as smart as hers enjoys a good challenge, and dealing arms while staying one step ahead of Interpol is a high stakes chess game. She'd enjoy it. To the contrary of that, printing money would bore her to death. After all, doing that she only had to get it right once. Print money so perfectly no one notices and... no one notices. She can print out a mint and spend it and have no challenge in it. If she gets it wrong, there's no profit. Selling arms? If she does it perfectly, people will notice but not catch her. If she does it wrong, she can still make money but have to escape. Much more challenging to someone with the brains and morals of a criminal mastermind but no urge to actually take over the world.