How to include a lightswitch for each related entry in the source element of a relationship
You are correct, you would not want to add those fields to the news items directly. Like you said, it would cause problems if you wanted a News item pinned on one service but not pinned on another one.

The best solution here (imo) is to utilize a Matrix field (or possibly a Table or SuperTable field, depends on your preference). So I would create a Matrix field for your service entries called News Items or whatever. Than each news item block would have several fields:


the actual related entry field where you would pull in the news entry
a lightswitch field for pinned
a lightswitch field for alert
a date field you could use to expire the news block
etc...


This would enable you to set these settings on each news block on the individual service entries, so you're not muddying up the news items themselves or contaminating other service pages where you may want a news item "pinned" or "alerted". And again, you could also use a SuperTable or maybe even a Table field instead of Matrix - just depends on what you prefer.