My question is, if it is a whole step between the first and second intervals in BOTH the major AND minor scales. Then how and why do we call the second interval a "Minor" 2nd if it is flattened half a step? The minor scale simply doesn't have a flattened second so why do we label it as if it does?
"We" don't. In both the Major and Minor scales, the interval from the Tonic (first degree) to the Supertonic (second degree) is a WHOLE step or Major Second.
If you want to know 'why' one scale is called Major and the other Minor (let's assume the Tonic is of the same pitch) is because the three intervals: 3rd, 6th and 7th are Major intervals (in a Major Scale) or each lowered a half-step to Minor intervals (in a Minor Scale). No lowering of the 2nd in either scale.
Using everyone's favorite scale based off C:
C Major - C, D, E, F, G, A, B, C
C Minor - C, D, Eb, F, G, Ab, Bb, C
The 'rule' is this:
When Major intervals are lowered one half-step they become Minor. Usual intervals: M2nd/m2nd, M3rd/m3rd, M6th/m6th, M7th/m7th, M9th/m9th, M13th/m13th. A few examples would be: C-E (M3rd)/C-Eb (m3rd); C-A (M6th)/C-Ab(m6th)
When Major intervals are raised one half-step they become Augmented. Usual intervals: M2nd/Aug2nd, M9th/Aug 9th. An example would be: C-D (M2nd)/C-D# (Aug2nd).
When Perfect intervals are lowered one half-step they become Diminished. Usual intervals: P5th/Dim5th. An example would be: C-G (P5th)/C-Gb (Dim5th).
When Perfect intervals are raised one half-step the become Augmented. Usual intervals: P5th/Aug5th, P11th/Aug11th. An example would be: C-G (P5th)/C-G# (Aug5th).
When Minor intervals are lowered one half-step they become Diminshed. Ususal interval: m7th/Dim7th. An example would be: C-Bb (m7th)/C-Bbb (Dim7th)
These rules also works in reverse.
Sure you can throw in Augmented Unisons, Diminshed 4ths, etc - but you won't find many examples.