I've make a quick hack to the module to make it to work properly both with magic_quotes_gpc() enabled and disabled. It'll be available in next daily built. For your info I've slightly modified this files:
and replacing your current files (don't forget to save them safely before) such problem should be out.
About how to solve the all those entries currently incorrect, the easier thing to do would be, once installed the last version, to edit and save each problematic page. New version should be correct. Also, you could perform some direct database
updates to solve it (basically, replace each occurrence of \" (backslash+double quotes) to " (double quotes). The SQL
sentence to do that against ALL your wiki pages is:
UPDATE mdl_wiki_pages set content=replace(content, '\\\"', '\"')
although you can restrict such update to only your problematic wiki by adding some condition like:
(where XX is the id of the wiki that you want to update)
Anyway, don't forget to make a copy of your table before executing the statement above. Direct handling of DB doesn't seem to be a good idea!
Hope it helps, ciao