We know that some people do eat real meat in the TNG universe - but it's pretty rare - because Keiko was disgusted when Miles told her that his mother cooked with real meat. (Unless that conversation was implying that Keiko was a vegetarian - which may be true as well...
But taken with Riker's comment that they eat something as tasty as meat - but no longer enslave animals for food...leads me to think that what they eat - and cook with - for the most part is either some sort of tissue culture (aka vat grown) meat...and/or possibly *replicated* cuts of "real" meat. Both are meat...but no animals are killed. (But maybe Keiko, being a vegetarian, is even grossed out by that...or maybe she just meant meat from live animals...?)
As for replicators in TOS time...sorry, but Janeway in "Flashback" already stated that replicators didn't exist in TOS's time - even in the TOS movie time. (And we saw kitchens on the Enterprise in TUC.)
We do know that they had "food synthesizers" even back in Enterprise's time...so likely what TOS had was a more advanced form of those.
Yesterday I saw a vending machine that could mix flour & quick yeast into dough, and make that into fully cooked & topped *pizza* - all in a few minutes...in 25 years...combine that with thinks like 3D printers - which *already* can make "cubes" of printed food (Hey....wait...food cubes!?)...and micro-machinery and molecular synthesizers...who know what would be possible!?
Now...as for the replicators turning energy directly into matter - as opposed to taking a store of matter, then using the transporters to convert it into energy (and/or a matter stream or data stream or whatever) and converts it back into matter - but re-arranged...well, it's likely they do that latter.
See...the Enterprise can convert tiny amounts of matter and anti-matter into ENORMOUS amounts of energy thanks to e=mc^2...but, that equation works both ways; just as tiny amounts of matter can be converted to enormous quantities of energy...it would take ENORMOUS quantities of energy (mindbogglingly huge amounts) to make even a tiny bit of matter.
SO for every cheeseburger you replicated - the Enterprise would need to convert a cheeseburger's worth of matter and anti-matter into energy for every cheeseburger you ate. Plus it would have to store all that extra anti-matter somewhere. Not to mention, store ALL of that energy needed for the replicators...somewhere...
Far easier to store bulk matter somewhere....then use the transporters/replicators to convert it into an energy-matter stream, rearrange it, and re-convert it into matter again. (Hence the lines that the replicators convert matter into energy...they do...as part of the process.)
They probably use stores of the base materials for making proteins and carbohydrates and fats and stuff...carbon and water and such...recombined into those forms...as well as other base elements - this would be the least energy
intensive. Maybe they even have some stores of proteins and fats and carbs and sugars themselves...but really that's not necessary once you have the atoms they are made of.
Turning atoms into other atoms would take more energy, but as it's been stated that they also can synthesize virtually any element or substance needed...the replicators are probably capable of a form of nucleosynthesis when it's necessary to create an element that they don't have, or are out of.