I mean, if you look at the dictionary definition.
"a person who is
admired or
idealized for courage, outstanding achievements, or noble qualities."
Who is a hero can change from society to society, time to time, or even person to person based on changing values or ideals.
The kingdom only values results, which is why the hero can be changed. So the alchemist is correct since the "hero" path in this instance isnt defined by good or evil.
If we go by your idea of a hero then Toni and his party aren't heroic either with the underhanded methods they used to usurp Allen. If its a case of "ends justify the means" then why would Toni be more of an ideal hero than Allen? Just because Allen is more blatant?