I had the same issue with the SD card freezing too often in games, so I've made a small program that write a small file on the SD card, and this completely fixed the issue!
I used the sources of an old program of mine, so the code is not pretty, but it does work fine:http://neko.works/u/hddping.zip
You can close the program using the notification icon, the app is named "SyStatus" (which is the name of my old program I've modified).
Note that this will write a file named "ping" on the SD drive. Use the relevant executable depending on its letter: I've prepared 3 alternatives for drive D, E and F.
If your SD card isn't on these letters, just use an hex editor on the .EXE and search for "E:\ping", replace "E" by your SD card letter as shown on the screenshot bellow.