One, why was the money given to Japan? That is an important piece of information need to make an informed opinion. Plus just because one country gives another money does not make that country more politically sympathetic to the other. Japan may have some issues like every country but it's still a pretty progressive one (as far as I know I am not from Japan so I do not know that much about them politically). The two countries need to have more in common than a gift of money before we need to worry about Japan becoming allies with North Korea.
While I do wonder about the underlying motives of this donation, I don't think it's really enough to make a country beholden to another. In the grand sceme of things, $500,000 isn't really that much. Sure, it's nice of North Korea, but I don't think it's a high enough amount to sway Japan's feelings.
No, Japan will not become too sympathetic towards North Korea simply because that nation gave them a large sum of money. The people and politicians of Japan are aware of North Korea's stand on many things. They are not going to be duped by a mere sum of donated funds.
No, this donation North Korea made to Japan seems like a lot of money to most people, but it's actually a token sum for governments, so if they intended to buy sympathy from Japan, they certainly didn't buy very much. North Korea isn't known for having goodwill towards the rest of the world, so I don't expect this donation to cause Japan to show much sympathy towards them.