Not saying anything bad WILL happen, however I have a new 15" Core i5 MBP and an i7 iMac and encoding takes a good bit of CPU power and creates a generous amount of heat. A desktop Mac generally has better ventilation to perform such tasks, especially if you're going to leave the computer unattended for an extended period of time. The only time I would do any encoding on my MBP is when the iMac is busy with other tasks and I'm just going to encode one or two movies. My main concern is overheating, shut downs and kernel panics.
If you absolutely have to do this with your Macbook then I would recommend to leave the screen open, as closed lid operation will transfer too much heat to your screen since you're going to leave it alone for the weekend. Also you should use SMC fan control to keep it as cool as possible. Just be cautious.