Nice to hear that the EyeFi can be used this way, I know there's been some discussion about it before!
As far as I know, there is no way in current CHDK releases to delete images the way you describe. There are some builds (more or less development test ones) which are capable to switch some camera models between rec and play modes, but I'm not sure if the S3IS is one of these. Switching to play mode and emulating the erase key presses would work for you, and it will be possible to do some day in the future.
The other option would be to develop file better file i/o and file system manipulation commands to uBasic/Lua. This is not a new feature request, but this EyeFi thing might speed up things on this part, especially if someone capable of adding those commands purchases one...
But there's a third option which might work with any build. I didn't try this, but here's a description of how it could work:
1) Enable the camera feature where the camera keeps the photo reviewed on LCD as long as you hold the shutter down. I think that's the default at least in A series cameras (specifying a N second review time doesn't disable this feature either).
2) Do not take the picture with the "shoot" script command. Instead, use
press "shoot_half"
rem wait for exposure etc; this could be replaced with a shoot state wait loop if power consumption or speed is an issue
sleep 5000
press "shoot_full"
rem wait 5 minutes with camera in review mode (hopefully it stays there that long?) for EyeFi to do it's magic.
sleep 300000
click "erase"
sleep 500
release "shoot_full"
sleep 500
click "set"
This code uses the camera feature where you press the erase button to delete the photo you just took, as long as you press the erase key before releasing the shutter. The above code keeps the shutter down for 5 minutes for your EyeFi to get the image, then presses erase, releases the shutter and presses func/set button. If your S3 post-shoot erase functions with different keystrokes, you need to do some changes, obviously.
This might work, but I didn't test any of it so don't get your hopes up too soon... I'm not even sure if the camera writes the jpeg before you release the review mode (it says it's deleting the image but you never know), and I'm not sure whether you can keep the camera in review mode for five minutes either or if there's a timeout for that.
Let us know if it works, I think there is some common interest for this.
