The base monitor service does nearly all the work, including sending the emails.
If your need is just to disable the emails for a specific period of time then it's possible to do this by updating SQL Monitor's data repository directly from your scripts.
Turn emails off (globally):
Turn emails back on:
I've tested this and it seems to work. Data collection is not stopped so there won't be any gaps in your data. Alerts are generated and will appear in the Alert Inbox (on the website). They just don't get emailed.
SQLCMD can be used to run the SQL from your OS scripts I believe.
Hope this helps