posts_join & posts_where : limit them to the posts selection only

I’m “hacking” a query using the posts_join & posts_where filters. Problem : this applies to each query on my wordpress, not only the posts selection.
For example I use a custom query to count my (custom) posts; and it is filtered by thoses filters.

Currently I find a solution adding those filter on a hook (before my posts query) and removing them when the query is done. But is there a “cleaner” solution ?