GUIMiner Scrypt is just a front-end for cgminer or reaper. I'm not sure which one you're using, but if you're using cgminer you can set intensity to "d" for dynamic, regardless of whether or not you're doing scrypt or sha256 mining. I don't use GUIMiner but I would imagine it has somewhere to set this. Keep in mind that with cgminer, I believe sha256 has intensity range of -10 to 14 and scrypt has an intensity range of 0 to 20.
Also if you use cgminer you can use CGWatcher to monitor the miner (and as a GUI) and there is an option to raise intensity on all GPUs to a specific value when the computer is idle, and it will lower them back to their original settings when it is no longer idle. This allows you to get higher hashrates during idle than dynamic intensity would. There are many more features, you can check the thread for more info:
https://bitcointalk.org/index.php?topic=185553.0And because GUIMiner Scrypt is just launching cgminer hidden, you can still use CGWatcher with it... although it will communicate and control cgminer only and has no interaction with GUIMiner. I've heard others mention this works but haven't tested it myself. This is assuming you've set GUIMiner to use cgminer and not reaper.
Edit: I should point out that I don't use dynamic intensity, but as I was writing this I set one GPU to "D" while scrypt mining and cgminer lowered it to 8, causing hashrate to go from ~400Kh/s to 20Kh/s. Temperature was not a factor because it was down to < 60C by the time I noticed. So either I need to adjust something in my config or cgminer is setting dynamic intensity based on sha256 intensity range and not adjusting for scrypt's intensity range.... maybe. I can't say that for certain and I'm too tired at the moment to look more into it now. I'd still suggest using cgminer and setting a specific intensity value, then setting CGWatcher to raise intensity when the computer is idle.