If you select all of the stored procedures in enterprise mgr, and generate one sql script for all drops into a "DropAllProcs.sql" and then generate one sql script for all creates into a "CreateAllProcs.sql", then you may be able to:
1. drop all
2. use search / replace in the "CreateAllProcs.sql"
to add the with encrypt
3. run the modified create all script
Hope this works for you (that is, if you only want a mediocre level of protection.)
HTH.
-Stephen