The tool you used - named "clear rude or abusive/spam flags" - does a lot more than just dispute pending flags and undelete the post. Before we start messing with it, let's consider the purpose it was intended to serve...
For the sake of readers who may not be familiar with the tooling here, I'll give a brief summary of the options you had available in the scenario you describe:
Flag in kind - this is most appropriate when the post being flagged is actually spam (or actually rude, or actually abusive): the moderator simply raises a flag which matches that already on the post. In response to this, the post is deleted and locked, the author is docked 100 reputation points, and the flags are marked helpful.
Delete or close the post - when done by a moderator, these actions implicitly mark any pending flags as helpful, but do not apply an additional penalty.
Mark helpful - this is an option any time there are pending flags (of any sort) on a post. It just marks the flag as helpful and does nothing else; most important for spam or rude/abusive flags is the fact that it doesn't cause the post to be deleted, locked or the author penalized in the way that actually flag-deleting the post would.
Decline - like "Mark helpful", this is an option for any pending flag. It marks the flags as declined (with an explanation chosen by the moderator) and leaves the post unmodified (apart from invalidating the automatic downvotes that are coupled with a spam or rude/offensive flag being raised).
clear rude or abusive/spam flags - this is ONLY available on posts that have either pending or helpful spam or rude/abusive flags. It marks those that are pending "disputed"... But it also goes back and retroactively changes the resolution of all past spam or rude/abusive flags on the post to disputed, unlocks the post (if it's locked), undeletes the post (if it's deleted), retracts the reputation penalty from the post's author (if it was applied) and invalidates any automatic downvotes.
Now... That last option - which is the one that inspired this request - is a very odd tool indeed; not only does it make extensive modifications to the post (and author's account), it re-writes history! No such option is available for any other type of flag; no matter how much you might regret fat-fingering a Not An Answer flag or disagree with another moderator's decision on a Very Low Quality flag, you can't go back and change the resolution once it's set.
So why does this tool exist? Why doesn't a similar option exist for other types of flags? That should be pretty obvious: it's that -100 penalty. That's a heck of a whammy for a mis-click, especially if (as is often the case) the author is a fairly new user. No other type of flag carries quite the same potential for misuse, made all the more dangerous by the fact that ordinary users can apply the same penalty simply by flagging the same post 6 times.
In short, this tool exists - and does everything that it does - because those actions are what is necessary to reverse mistakes.
...which also suggests you were misusing it. Nobody made a mistake; the post was flagged because someone thought it was rude - either you agree or you don't, but there's no damage to undo. You could've either declined it (if it didn't strike you as rude) or marked it helpful (if the post was kinda rude) - the latter would've respected the flagger without penalizing the author who presumably realized his own mistake.
So, given the two options available on every type of flag would've completely side-stepped this problem... Why did you instead opt to use an obscure tool that exists only to patch up grievous errors? I think Brad suggests a possible answer to that in the comments above:
[...] If a moderator wanted to clear the spam flag (not declining, maybe because there was something slightly spammy about the question even if it wasn't spam) it would immediately undelete the post. [...]
You probably did think the post was kinda rude. Maybe not rude enough for the entire "-100 locked deleted" treatment, but... still pretty rude. So you didn't want to decline the flag. Now, this is what "helpful" exists for, but you're probably thinking "if the post wasn't already deleted, I wouldn't mark this helpful because it's not quite rude enough" - so you avoided that option too (even though it would've done exactly what you needed).
What you wanted to see was a third option, some sort of "dismiss as kinda sorta correct but not entirely" - which is sorta how "disputed" is usually interpreted. Nevermind that you're not actually asked to judge the objective correctness of flags so much as to indicate whether they're helpful; both flaggers and moderators often interpret flag statuses as a commentary on the moderator team's view of the world at large, so even unhelpful flags that aren't acted on must be marked helpful if the post matches some pattern and even helpful flags that bring to your attention a matter which requires your intervention must be declined if the post fails to contain a certain keyword. Or something.
...which suggests that what we actually need here is a revision to the guidance presented to moderators in the UI that better indicates what the various options really mean.