Based on similar re-mappings in other programs, this may be difficult to get it to work the way you would like it to. I don't actually have Maya to play with for testing this out, but I'm pretty sure you should be able to get something to work one way or another--not impossible but it may take some experimenting.
One thing to keep in mind with panning replacements is that you may need to use additional hotkeys for "Up" functions. Once you add an "Up" function the original/non-"Up" function is implicitly handled as a "Down Only" function.
Try something like this below. You may need to add {Ctrl Up} to the first hotkey as well if it isn't automatically sent when the hotkey is triggered. Use the tray icon to open the program and look at the keystrokes that get played back if it's not doing what you think it should be doing
#IfWinActive, ahk_exe maya.exe ; ← replace with actual exe name
^!LButton::SendInput {Alt Down}{MButton Down}
^!LButton Up::SendInput {MButton Up}{Alt Up}
#IfWinActive
In your original script:
^LButton::MButton
...you may want to look at two things:
1) Adding a * modifier so it will be active no matter what other keys are pressed
2) Looking at the keystroke log. What I would suspect happens with this single hotkey, is that--without a corresponding "Up" hotkey--as soon as you click down on LButton while holding control, the keys sent are
- Ctrl Up
- LButton Up
- MButton Down
- MButton Up
i.e., even if you are still sitting there with LButton held down, it may already have been programmatically 'unclicked', and 'MButton' may not be held down necessarily. This is mostly just a guess though, see the keystroke log for exactly what's happening or not.