TL;DR: I suggest to blacklist the deprecated tags that still exist on some questions, in order to prevent them from being added to new questions.
There are a few tags which are deprecated and should not be used at all, but still exist on the site.1 Ideally such tags should be completely removed, but this would require at least some manual retagging, so it's probably not going to happen anytime soon.2
On the other hand, it might be useful at least to prevent these tags from being added to new questions. (At the moment, the new questions are usually retagged by some users. And since not too many new questions have some of the deprecated tags, it seems that the users who do this are doing quite a good job. Still, if addition of deprecated tags is prevented by software, those users could direct their energy to other - possibly more useful - activities.)
A possible solution to this problem could be blacklisting those tags. I will stress that blacklisting a tag does not mean that at the same time the tag has to be removed from all questions.3
Blacklisting causes that the tag cannot be added to new questions and when a question with a blacklisted tag is edited, the edit cannot be saved with this tag still included. In both cases, a warning is displayed - it can be a generic message used for blacklisted tags, but it can also be customized. So in this case it might be reasonable to list some of the most common related tags in the text of this warning. (In fact, including tag warnings for deprecated tags has already been suggested before: Tag warnings on MO.)
Some basic information about blacklisted tags can also be found in the corresponding tag-info.
Proposal: Let us blacklist the tags which are deprecated but still exist on the site. In the future, if some other big tags are deprecated, blacklisting should be considered as well. (At least in the cases when the removal of the tags is likely to take a long time.)
NOTE: This post is not intended for discussion whether or not those tags indeed should be deprecated. When I look at the tag excerpts, I see that information that the tag is deprecated was added in March 2016 for abstract-algebra, in February 2016 for discrete-mathematics and in June 2013 for geometry. So the decision that these tags are deprecated were made quite a long time ago and this can be considered established practice. (If somebody thinks that some of these tags should not be deprecated or wants to know more about the reasons why there are deprecated, it would be better to make a separate post for such discussion.)
1Theoretically moderators could request from SE staff to burninate the tags or they could merge them into (tag-removed). So hypothetically it is possible to remove all instances of a specific tag without bumping any old questions. However, for big tags such removal would likely end up with many questions missing relevant tags and being tagged incorrectly. I suppose that this is the reason why some tags are still kept despite being deprecated. (But I was unable to find something here on meta where this was discussed in detail.)
2At the moment there are about 900 questions with deprecated tags. (At least the ones I am aware of.) Considering that there were 1000 such questions in August 2017, the number is not decreasing very fast.
In fact, it seems that the main contributing factors to the decrease was that the number of questions in geometry tag dropped. This was partly thanks to bunch of retags made by François G. Dorais. And partly thanks to the fact that some questions were bumped in order to replace images that were no longer displayed. And after those questions were bumped, quite often also the deprecated (geometry) tag was replaced by more suitable tags. (For example, Joseph O'Rourke and j.c. updated images in many of their own posts. And I have also seen several such edits by jeq - if you check list of their edits, you can find several such edits - just search for the edit summary containing: "Copied image to imgur.com, as it was not being displayed because of the new https rule".)
In case somebody is interested in more detailed stats, you can check them here in chat.
3In fact, for a long time I did not know that blacklisting is possible even without removal of all instances of the tag. I find out about this only after Asaf Karagila posted this feature request on Mathematics Meta: Can we please have a “deprecated tag” feature?