It's safe to disable the plugin since you no longer see the old URLs in the index.
To be even safer I recommend doing the following:
- submit a sitemap containing only the new URLs
- make sure that all inbound links use the new URLs.
- create a custom 404 page which mimics your sitemap. This is in case your backlinks uses the old URLs. You would want to send the user a friendly page to help them find what they are looking for.
- Help the Google robot by having the correct canonical tags.
EDIT on handling old URL and backlinks you want to preserve:
I had a chat with an SEO consultant about your matter and here is a possible course of action:
The main solution is being able to handle traffic coming from a referring link on an external site and handling an old indexed link coming from search, then trying to come up with an elegant WordPress solution for it.
The first step is to go into Google Analytics and figure out which links are the most landed on both traffic mediums and to do that you will have to create an Advanced Segment, located on the upper right of the reporting profile. Once there you would have to create:
Traffic Sources > Medium "Matches Exactly" > referral
Traffic Sources > Medium "Matches Exactly" > organic
Once you've created both go to the Content > Top Landing Pages and look at the top 15 to 20 pages on the report. Sort through the list and find out which ones are 404's and the next solution would be different for both traffic mediums.
For Referral traffic, you would have to create a rule where if visitors came from a Referring site and the content doesn't exist, point it to the best relevant content based on text on the referring URL from the visitors cookie, which would be a Search Results Page (SRP) on WordPress. Now this is a complicated but elegant solution. If you can't pull this off, just create a rule on the mod server file to handle x amount of visitors landing on old page to land on new page.
For Organic traffic, which would be slightly easier to handle, you would have to get the original keyword that brought the visitor to the old indexed link from the search engine and then pass that value over to the WordPress content search engine, in essence landing them on a SRP page. You must be careful though to only do this for links that doesn't exist anymore and if the visitor came from search.
What's the best way to figure this out? Manipulating and using the GA cookie values. The GA tag is smart enough to define where the visitor came from and what medium, to see this download and install Firebug (or any HTTP debugger). Look for the GET request being kicked off by the __utm.gif file (the GA tracking pixel), then look at the values. You would see from a parameter list how your visit (or anyone else's) are being identified by GA.