Tosfos clearly is aware of this when he says "v'Ein Beki'in Pirush Ein Choshishin" -- "and Ein Beki'in means they are not wary (of the Derasha)." Tosfos' usage of the phraseology "Pirush" -- "this means" indicates he is going to say an explanation that is not based on the regular simple meaning of the word. In fact, the Yerushalmi here says a similar explanation. It is possible that this is not such a difficult explanation, as Tosfos may mean that they know of the Derasha and understand how it is made from the Pasuk, but did not hold that it had Halachic significance. They probably understood that it was more similar to an Asmachta, or that it was not a main meaning of the Pasuk. "Ain Beki'in" indicates that they were not aware of the importance of this meaning in the Pasuk, as opposed to "Lo Kiblu" which would mean they knew of those who make the Derasha and fully rejected it, holding that it cannot be the explanation of the Pasuk.

All the best,

Yaakov Montrose