Actually you don't need the extra parentheses, !c("A", "B") %in% c("B", "C")
works.
If you prefer something that reads easier, just define it yourself:
"%nin%" <- function(x, table) match(x, table, nomatch = 0L) == 0L
This has the advantage of not wasting effort -- we don't get a result and then negate it, we just get the result directly. (the difference should generally be trivial)