On a multisite, if you update to 4.3.1, then the "upgrade network" process will do the job for you there. The code in my last post here is the new code that will be included in 4.3.1 to clean this mess up.
If you are trying to clean it up now, and you are using the above code in a mu-plugin, then "upgrade network" will essentially cause a ping to each site which *should* run the mu-plugin code as well. However, if there is nothing for it to actually upgrade, then I don't believe it will actually ping each site.
The above code should cause no additional load, since it's performing only one query to get the cron data, and one additional query to save it back, if it needs to remove the extra entries. So, you can leave it running for a little while and allow normal traffic to the sites to clear the problem up for you.