To be honest, there is no completely reliable method to ensure that you don't delete stored procedures that are being used.. Consider the fact that some stored procedures may be used only monthly, quarterly, or even only yearly.
About the best way to ensure that you don't delete something that you need is to append the stored procedure names with DeleteOn_yyyymmdd where yyyymmdd is a date a year into the future and prepend them with "zzz_" to kinda of move them out of the way in the SQL Explorer window and to make it apparent that you don't think they're being used and will be deleted.
I also do similar with view, functions, tables. The programmatic stuff doesn't take much room but tables can be a pain. I make a scratch and arch schema on each database and tell folks that for tables they only need for a week, to create them in the scratch schema and for things they'll need for 13 months, put those in the arch schema. I wrote an automatic "rake" that will rename to identify they're going to be deleted after a week and after 13 months respectively and, once renamed, wait for a week and then drop them unceremoniously.
If you absolutely need to get them out of your database, start a small ToBeDeleted database and put them there along with the renaming as before.