[RPG] What are CR-appropriate spell effects

Your ruling is unlikely to break anything. However, the rules on their own (and the underlying fictional significance of the rules) appear to answer this with a No.

The surface rules difficulty is that a there's no object duplication involved — you start with a spell scroll and end with a page in a spellbook. These aren't identical objects, as the ability requires.

One might argue that they are the same, just with one bound into a book and one not, but spell scrolls and spellbook pages aren't functionally interchangeable either. They function differently and contain different information: you can cast a spell off a scroll, thereby destroying it, but you can't cast a spell off a page in a spellbook in the same way (and if you do it as a ritual it works differently, and doesn't destroy it); similarly, understanding the scroll is harder than understanding the page in the spellbook. The two objects are distinctly different and the kenku's particular skill doesn't come into play.

But this mere rules difference reflects a deeper meaning: how learning spells from scrolls works in the fiction. The normal process of “copying” a spell from a scroll into a wizard's spellbook actually involves a translation: from how the scroll presents a ready-to-cast spell, into a record of the wizard's own personal understanding of the nature and process of preparing and casting the spell. The Arcana check for copying appears to represent the possibility of failing to extract the necessary understanding of the spell from the scroll's not-a-spellbook formulation, and thus the possibility of being unable to scribe the spell due to simply failing to actually learn it from the scroll. Being good at duplicating things doesn't help with learning arcane secrets of the universe.

The rule is an extension of a precedent set by WoTC themselves

The lead rules designer of 5e, Jeremy Crawford, has¹ the power to make official rulings, and frequently does so on Twitter, and in the Sage Advice column on the official D&D site. It's common for him to answer questions with some variation of "if a feature was meant to work that way, it would say so." He has even explicitly stated:

Beware of claims that a rule does something mentioned nowhere in that rule or elsewhere in the core books. There aren't secret rules. (source)

Using this principle, he has made rulings such as:

The Dual Wielder feat doesn't include the benefit of the Two-Weapon Fighting feature. It would say so if it did.
(source)

or

If the grease spell created a flammable substance, the spell would say so. It doesn't say so. (source)

From this, we can derive that barring some explicit clarification from Sage Advice, JC himself, an official errata, or a more specific rule mentioned somewhere else in the game's official material, features in the game are intended to only do what they say. Though, of course, the DM is permitted to make their own rulings and allow spells and effects to do things not directly stated in their description as they see fit.

¹ _{While this status was subsequently backed away from (official rulings only now apply to the Sage Advice Compendium as posted by WoTC, not the tweets from J Crawford), it was true that his ruling was authoritative when this question was asked, and answered; that change in state does not change the overall point.}