Should be fine ... as long as you're sure this is a functional, equivalent HDD ... those subminiature HDD's are hard to come by.
Check out this site... it's about battery replacement but has excellent instructions and diag's for taking apart a 3G including removing the HDD which is necessary for battery replacement.
Edit: very nice ... I mentioned the site but forgot to post the link:
http://www.ipodbattery.com/ 