Finally we rewrited completly the Search & Replace plugin.
It's now very powerfull one, each tasks ( searching and replacing ) are done in a separated thread while the results view now use a custom model.
This allow the view to be updated more often without freezing the main interface.
New modes have been added:

• Search in project files
• Replace in project files
• Search in opened files
• Replace in opened files

As new options:

• Whole word
• Wrap

This is now the perfect search & replace tool in the wild ;)
It's available in the svn in v2/branches/dev.
Please test and report bugs.