It's a cool idea and surely the game can be easily modified to suit square bases - you don't have to use the slotted movement trays. As luck would have it, a tray of identical dimensions can accept eight 25mm based Warhammer miniatures. 20mm based miniatures have some extra space, but no big deal.
Monsters are the real issue, and would need to be compensated for having square bases instead of round to retain WOTR balance.
A nice idea, since yeah, many of the units are easy to convert. It's the points costs where the real balancing work would start. You shouldn't convert those. Also, you'd have to dig a bit deeper to the Warhammer lore to come up with Legendary units for all races...as well as hero-level named characters.
For example, here would be a statline for a formation of basic melee orcs:
M F S D A R C
6 3/5+ 4 5 8 1 3
Wargear: Hand weapons and armour
Note that there is a bit of variation added: Fantasy (and 40k) could do with a bit more differentiation and this is true in the orcs' case, to be honest they're worse shots than humans (not enough to warrant BS 2 which is very bad in the system), and they really have strength 3.5 in FB, and the Choppa rule represents that, but in WOTH they can be S4 without worries. The really tough S4 units in FB (like Ogres) would get S5 and so on.
Also note that WOTR effectively has, three levels of armour, the ones that grant 1 or 2 defense are called "armour" and the one that grants 3 is called "heavy armour". The orc here has the armour that grants 1 defense eg. light armour.
An easy rule of thumb is that sparse or leather armour grants 1 def, mail or scale usually grants 2, and full plate / gromril / chaos armour grants 3.