The alternative would be to wait until you weren't doing anything important, and had nothing important on the horizon - which is when your employer will be thinking of you as a dead weight. If you're a valuable employee, then you'll always be working on something that your employer values. It's far better to move on when you're the star performer and they're sorry to see you go, than when you're the slacker that they can't wait to boot out.

Things look a bit different from the other side of the table, anyway; the original questioner's project is a tricky one but it doesn't sound like it's absolutely critical to the company. If he's not around then they can probably make do with somebody else (maybe a new hire), or just live with the old system. People come and go for all sorts of reasons, and it's the responsibility of management to cope with that. As long as he gives reasonable notice and cooperates with the process then there should be no grounds for hard feelings.