I keep thinking about how the meaning might change if you switch が out with は in this phrase

The sentence goes like「待っているのがあなたじゃなければ…」

The official translation was "If you weren't the one [she] was waiting for…" like I vaguely guessed.

But now if it was は instead, wouldn't the usual way of interpreting 「待っているのはあなたじゃなければ…」be "If you weren't the one waiting…"?