Max M. answered 05/22/19
Harvard Literature major with 20 years of coaching writers
Well, only Rowling knows for sure, but there certainly is plenty of wordplay and allusion in the Potter series, from spells with obvious Latin derivation--e.g., lumos, petrificus totalus, etc.--to less obvious ones--e.g., tarantallegra comes from the lively dance "tarantella" and Italian for happy or fast--to names--e.g., Lupin comes from the Latin for wolf, Sirius is also known as the dog star, and even Fawkes the phoenix may be named after Guy Fawkes, who tried to blow up Parliament in 1605 (and every so often, Fawkes the phoenix blows up and is reborn)--and so on.
Personally, I sometimes wonder how much of the mythology of the series was worked out beforehand. For instance, did Rowling know the invisibility cloak was a deathly hallow when she introduced it in book one? If so, why did no one comment on its extraordinary resilience at the time, the way they do in book 7? Did she know the diary was a horcrux when she introduced it in book 2? Or did she incorporate those into the mythology as she developed it? (And this is not to mention inconsistencies people like to point out like, why didn't Fred and George notice Peter Pettigrew hanging around Ron on the Marauders' Map?) Again, only she knows for sure.
So the question about the flowers seems to hinge on how worked out Snape's history was from the beginning. I would guess, pretty well worked out. The idea of Snape as a double agent under deep cover doesn't seem to have any inconsistencies, and the explanation for it seems to be woven consistently through all the books. Remember, we find out Snape isn't evil by the end of book 1, when Dumbledore explains that Snape was trying to protect Harry rather than stalk him. So a not-evil character hates Harry but consistently protects him. Why? I would guess that the answer "unrequited love for his dead mother" was probably there from the beginning.
So was the flower question deliberate? Given how much Rowling clearly likes peppering the story with both obvious and obscure references to Greek, Roman, Norse, Germanic, Celtic, and English lore, I think it's very very likely it was.