It's not always Major. If you're starting from something that has no Body score to speak of (the bean in your example) or if you're adding a new skill/ability to something that can't normally do it (allowing somebody to fly, to to become invisible) so that you're using an Innovation miracle, then yes it's Major. (And has a base cost of 7--Innovations take more divine oomph than Alterations.)
However, if you're starting with something that CAN perform the activity and you're merely *improving* that ability, then it's an Alteration. And the power of the miracle depends on how many die steps of improvement you're giving it (per the middle portion of the unnumbered chart on p83 of the NGH).
So, checking the chart, we see that if you're improving an elite warrior (Body d8) up to d10, for 1 die step of increase, that's a Minor Alteration (base cost 3). If you're starting with a generic human, you need 2 die steps of increase and need a Significant Alteration (base cost 4). Or, to turn a Stereotypical Little Old Lady into a Olympic Decathlon gold medalist (d4 boosted to d12), that's 4 steps of increase and requires a Legendary Alteration (base cost 6).
And yes, near as I can tell, boosting someone's Scale without changing their die size is a Trivial Alteration. I also begin to think it's a primary candidate for min/max players (like myself...) to use in "breaking the game". Especially in concert with the "use as many dice as the opponent" rule called out (quite reasonably in context) on NGH p83 and then extended to Heroes (rather inadvisably IMHO) on NGH p89.
Imagine what, say, Glen Welch could do using that rule on his home territory with a Major Domain of, say, 'Embarrassingly-Humorous Death', in Harmony with Control, and ... a chipmunk. Boost 'munk to Continent scale fighting knowledge/ferocity for a great whomping 4 Belief (base cost 2 for Trivial Alteration with a Cost Factor of 2--5 for Scale less 3 for Domain and Inclination), then throw it at the oncoming 7000-strong Territory-sized salamander army. The only thing remaining is for the humans to establish whether salamander-slaw really DOES taste just like chicken.... (Okay, he *might* need to follow up the Chipmunk Of DOOM with a Vorpal Kitten in case they're not ALL dead after round 1...but it's unlikely.)
Okay, getting off my soapbox now....