It depends on what exactly you're deducting for, or more specifically, whether it's something that's liable to change from one turn to the next. For instance, if you want to make a civ research more slowly when it's ahead in techs, don't deduct research points each turn; instead, create a no-cost hidden building that gives a -10% research penalty, then use Lua to give that building to all cities owned by whichever player is in the lead. And since you can declare a <NoLimit> flag in the building class, you can stack this building if you want it to be -50% for whoever's in first, -40% for whoever's in second, and so on. Or, if you don't like percentiles, you can make it a -5 research per turn sort of thing, but that obviously is going to have era-dependence issues. You can either do this on a city-by-city basis, or create a National Wonder that has an empire-wide research penalty, and place it in the capital. That Wonder option is a much better solution, usually, since it doesn't require a city-by-city check, but has a few other issues depending on whether the player has turned on things like the "limit one national wonder per city" flag. (Wonders also often have notifications.)
This hidden building mechanism avoids the already-complete issue you noted, and it also makes the "turns until complete" readout more accurate, since that'll now take into account the reduced research rate. The only real downside, besides the obvious need for a turn-by-turn check and reallocation, is that the city UI will show this penalty under the "from Buildings" line of the research popup, and if you haven't modded CityView like I have, it'll show up in your buildings-in-city list.
It's also possible to use Policies to slow down research in a similar way, although that really only works if your mod uses a "placeholder" hidden Policy, like mine do. Getting a hidden policy to work takes a LOT more work than a hidden building, but if you have the choice it's actually a better solution since there are no issues if a city gets captured.