I've always interpreted it as that Zeal, after hooking up with Lavos, acheived immortality, and thus, with that on her mind, completely forgot about her kingdom, and was blind to its destruction.
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And, if you consider that we see Queen Zeal as far as 2300AD into the future, at the Black Omen, when she lived all the way back in 12000BC, you must consider that she's lived...over 14300 years (I estimate she was about 40 years or older back when she acheives immortality), so of course you'd have to consider that she's acheived immortality! Of course, she's also probably become a part of Lavos, too.
Queen Zeal ~ The Bride of Lavos. R.I.P.