For linked servers, I see how it is possible to change the "remote query timeout" configuration to hint a call to a linked server should complete or rollback within the specific timeout value. This appears to work across the SQL Server engine--is it possible to change the hint within a stored procedure, so that a specific stored procedure could run longer if needs to, but all other non-hinted SPROCs would timeout quicker if they run long?
Linked Query Timeout is discussed here: http://support.microsoft.com/kb/314530
Example code to set it to timeout in 3 seconds is here:
sp_configure 'remote query timeout', 3
go
reconfigure with override
go
Not really advisable to change it within a stored procedure. remote query timeout is a global server setting when altered with sp_configure, so changing it in a stored procedure affects all remote queries for all linked servers on the server.
Additionally, executing sp_configure requires the ALTER SETTINGS server permission, which typically only sysadmin and serveradmin have. Granting these permissions to a data access account would be a security concern since they could potentially take your server down with sp_configure commands.
What I would suggest is creating a second linked server with a different name that you would use with just this one stored procedure. You can, in SSMS, configure a query timeout for each individual linked server. Adding a second linked server would enable you to query the same server with different linked server client settings. You might need to create a DNS CNAME to accomplish this if you're using plain SQL Server Linked Servers.