You ask, 'Is it worth to pursue a relationship that might not last?'.
No relationship is guaranteed to last. If we got hung up and didn't act because we kept asking ourselves this question, few people would be in relationships today. There's always a risk factor involved when it comes to relationships. Always. The question you should be asking yourself is, 'Is it worth the risk to pursue this relationship?'. It seems like you like her quite a bit... if you're asking yourself these questions you've mentioned, it supports that. Don't think about what may happen then. Think about what can happen now. If it comes to fall 2006, you can deal with it then. If you guys are that into each other... long distance can probably work.
The thing is, if you really want to pursue this relationship but don't because of your fear of what would happen come next year... you could lose your chance altogether. This could be a great relationship.. or maybe even what you've been looking for your entire life. That would probably be something you'd regret if you wanted to be with her but never did anything about it.
If a dream comes true... then is it still a dream?