I heard that HT in i3 can actually cause performance drops because software doesn't differentiate between threads and cores. So when the software tries to split the data processing between core 0 and 1 both end up on core 0 on i3 as two threads instead, while the other core does "nothing".
HT when it first came out on the P4 had a lot of issues. Not so much because of the problem you mentioned (although most P4s had only one core...) but because most programs weren't well threaded. Intels HT has been around a long time now and many programs are well threaded so there are few issues with using it. You can try it both ways if you want, but I'm certain that on will be better then off.