Your explanation was clear enough for me to understand - unless I actually misunderstood. I hadn't thought about this under that angle. (Infinity Mode has that same option, by the way.)
Though, wouldn't that count as an edge case? I mean, infinite researches have an exponential (or at least linearly increasing in the case of ERP cost) so in a non-cheat environment, that wouldn't ever be an issue. In the case of a cheating environment (with instant research) one would just have to disable Auto Research while doing it - given that they know about it so some kind of warning message would be necessary.
I could see that as a new "ignore infinite techs" checkbox, which is enabled by default. When you hover it, it warns you about instant researches. Something like "Using Auto Research with Instant Research from Cheat Mode will cause an infinite loop. Use at your own risks."
Alternatively, an input box that allows the player to set a number. After a research finishes, add 1 to a variable and when it reaches that number, Auto Research stops and resets the variable so the user can unpause AR for another round.
One last option that I can think of would probably be the simplest: ingredient limits. Either go by the max quantity of a single ingredient, or by the cost of the full tech. The mod would allow setting a custom amount - if a research exceeds that cost, it won't be started.
Just some ideas in case you want to consider the issue. Otherwise, instant researches not queuing aren't that much of an issue.