Why are size 6 cities your baseline for establishing the losses? The changes now reward having large cities, in particular the public school has been buffed quite a bit.
Plus, the specialist slots lost from the library are now added to research lab and to observatory. So for well-developed (and well-placed) science cities, you have lost no specialist slots -- they've just been rearranged.
So now you have to think about building big cities and trying to build/buy research labs in your strongest science cities. Running the numbers out, if you were the type who like to build large cities (10+ population with at least public schools) these changes only barely make your science less than before. In fact, if you're not running ALL science specialists ALL the time, the change to the public school alone makes post-patch large cities output MORE science than pre-patch. (If you calculate it out, ALL cities with no science specialists but with library+uni+publicschool actually output 25% more science post-patch than pre-patch)
For an empire consisting of a bunch of small cities (ICS style, etc.), yes, the total science will be much much less post-patch. For a builder-type empire consisting of some well-placed thriving cities, the total science pre-patch and post-patch is pretty close... and sometimes, under certain conditions, post-patch can actually be higher.
In general, yes, your total overall science may be a bit less, but it's only going to be as dramatic as you say it is if you just plain REFUSE to adopt new strategies.