I believe that Matthew Read is correct about there being no native way to sync this, and about Locale's ability to work around this, but I'm going to suggest some cheaper and simpler alternatives to the $10 Locale app:
Tasker ($6.50): Basically the same as Locale but cheaper. With this (and probably Locale) you could set a profile that turns on AutoSync for only 5 minutes and repeats this every hour (or whatever timeframe you want). Also, Tasker can use Locale plugins.
JuiceDefender (free): I've used it before (although never tried what you are trying to do) and it's super easy to setup and use. It allows you to control total connectivity and app by app connectivity control. It also claims to allow you to schedule "Synchronization Events", which I've never tried by sounds like it would control general and app specific syncing.
Sync Schedule (free): I don't think this will be as useful as the name suggests but if all else fails it's worth a shot. It allows you to set times for the autosync to turn off and on but I'm not sure if it lets you set multiple time windows per day so this may be of limited use.
Also regarding your "is there any way to make it pause when I actually want to use the phone?" question, the native Android Power Control Widget has an Autosync as one of the options allowing you to toggle it on/off at will.