Here's how you can do it,
1. Rename handbrakecli.exe to handbrake.exe in the MCEBuddy folder
2. Create a batch file with the above command and change handbrakecli.exe to handbrake.exe (add %* at the end of the command line to pass ALL the parameters)
start /affinity 240 "C:\Program Files\MCEBuddy2x\handbrake\handbrake.exe" %*
3. Convert the batch file to a exe file using
Option A - Advanced Batch to Exe converter - http://www.battoexeconverter.com/downloads/advbattoexe.exe
Option B - Use Windows IExpress tool - http://renegadetech.blogspot.com/2006/07/how-to-convert-bat-file-or-vbs-file.html
Both are free.
Name the executable generated from the above tools as handbrakecli.exe and place it in the MCEBuddy folder.