There isn't a simple "undo" that will achieve this, so it looks like you will be looking for the least hassle workaround to acheive the same result. There are always ways of fudging it, some are more hassle than they are worth, others work pretty well and are quick but have drawbacks:
You are aware of the ability to manually delete, but this is a multiple step process that could take a long time for established podcasts with many episodes.
You could delete the podcast, and then redownload the ones you are interested in, which will also revert the extra episodes visibility, but this will take extra time to redownload, and you might have to make a list of the ones you want etc.
So, still a workaround but the one that produces the results with the minimum of steps: Delete the podcast from your lists, it will ask you if you want to remove the files, or keep them in your itunes media folder. Select keep, then go to (Windows example, this may be different on your Mac) File > Add Folder to Library > Navigate to your iTunes/Media/Podcasts folder, and select it. This will rescan the contents of the podcasts folder, and re-add anything into your library that exists as a file, but is not already in your library (Don't worry, you won't get duplicates) - this will restore your podcast including all your downloaded episodes, and remove the list of other available ones.
On the assumption that you have the option for iTunes to organise your folders for you, the podcast should already have it's own folder structure inside the general podcasts directory, thus ensuring you only scan the folders you need to increase speed etc.
Note that any ratings, and watched flags etc will be reset by this method.
Alternatively you could always try to ignore the list, and create a smart playlist where Album = Podcast name, and Plays = 0 to show downloaded and unplayed episodes (or any other criteria, the smart folder will not search through the undownload extra episodes that are visible and so the results will be filtered from your downloaded episodes only).
This IS actually the case.
What you should have a look at is the selection option that you have set.
For instance, if you ask to only sync the "3 most recent unplayed episodes", it might be that the one you are listening to will be replace on your iPhone by the newly released episodes that have been downloaded in iTunes. When the episode you haven't finished will be one of the 3 candidates to be synced (i.e. "when you have listened to all the newer episodes"), the listening will continue where you were the last time you listen to it.
EDIT after the EDIT of the Question :
Hm, ok, with this edit my answer is not right anymore BUT i think you should have a way have it work as you want. If you select for instance "the oldest unread", the one you are listening to will be kept on the iPhone (if you listen to the episodes in order that they are realeased) Another trick is to use the checkboxes on the left of each episode and set the preference to "Sync only checked"
Best Answer
Apple hosts a directory, Apple does not host the files of podcasts.
If you update the file of a podcast on your server, but do not indicate that you've updated it in your RSS feed, then only new downloaders will get the new file (obviously). If you update your RSS feed to indicate that there is a new file, then many podcast catchers will figure out they need to re-download the file. Others will simply list it as a new file again.