Hi,
I think SMQ1 holds the entries based on Application wise not data source wise.
if yes then you better to deactivate your data source only.
If you need to remove your whole application data sources then you need to deactivate the all data sources at ECC side.
With doing any thing at data source then you can take abap expert and find how the system sending information to SMQ1 for specific application.Based on that investigation you will find the way to not to update records to SMQ1 for your application.
Even you need to stop update to SMQ1?what's the situation made you to take this action?
Thanks