I don't see anything wrong with that. It means that we are incentivized to build more libraries, which we want anyway.
It also means that Academies are even more massively expensive mechanically.
Building one Academy and Two Libraries costs us 3 secondaries, 9 culture, and 3 wealth, to give us +1 RA tolerance.
In comparison, building a GP costs us 3 secondaries, 9 culture, and 9 econ to give us +1 RA tolerance, +1 temp damage tolerance, +0.5 tech refund, +1 max Martial, and some fiddling with our cent range that mostly cancels out (+0.5 low cent tolerance, -1 high cent tolerance, +1/3 high cent tolerance via allowing admin-free True Cities).
Now, it is obviously true that not everything can or should be expressed mechanically - but it is generally a good thing for the mechanics to express the effects of our building, and the mechanics of the Academy are already expensive with the requirement of one matching library, much less two.
Because we cannot touch negative Econ and thus City Support allows us waaay mere leeway in turn plan. What we get at midturn is only half the story.
Colony taxes and refugee income offsets those costs directly; e.g. right now while sitting at 27 (+5) [+5-8], we can safely spend all 27 econ since our net income is +2. This has been confirmed by AN on at least one or two occasions.