Can cited works hold grammatical positions in sentences? Though I read this style quite often, I was recently told unambiguously by a reviewer that I was NOT supposed to use citations "as if they are objects in a sentence."  The following sentence is an example of what the reviewer considered unacceptable:  


  We analyzed the data using the Wilmerding method, guided by [12].


The references section might include the following: 


  [12] Smith, D., Marshawn, J., &amp; Devenshaw, A. 2011. Techniques and
  Procedures for Applying the Wilmerding Method.  Prince Publications,
  Inc, New York, NY.


The Wilmerding method1 is not a step-by-step algorithm that can be precisely followed as if by a machine, and thus [12] does not provide a step-by-step algorithmic description but rather guidance for using  the method. [12] is a relatively slim but authoritative textbook about how to use the Wilmerding method.

Within this question, for the purpose of discussion, I have intentionally put [12] in grammatical positions where it's an important element of the sentence and the sentence would make less sense without the reference.  Sometimes that seems to be the most efficient way to communicate the intended message.  Is using a reference as a grammatical sentence element like this OK?   Why might this not be considered acceptable?   Should I be rewording those sentences?  Is it enough of a violation to be worth passing the note on to authors of papers I review? 

I considered posting this on EL&amp;U but it seems more specific to academia than general English usage, and the comment came from a content reviewer rather than a copy editor.  This question is related but it seems to be more about when to put authors names' in vs. outside of the parentheses in an APA-like style. 

The numbered citation style (as opposed to following APA, for example) is required by the venue.

1: Fictionalized for the purpose of this discussion
Conceivably the reviewer objected to the non-mention of peoples' names, thinking that should write "guided by J. Doe [12]" or "guided by [Doe12]" or "... by [Doe2011]"... Something in that direction would be my preference, also, since numbers in a bibliography are completely artifactual, not really adding any information. Names are far more informative.

But, still, it's possible that the objection was completely stylistic, so ... "it's just a rule"... which means rational discussion of it is presumably out-of-bounds. Such things seem silly to me, but I am acquainted with people for whom such rules are the only defense against Darkness and Chaos, etc.

I'd not comment on such things in any review/referee-report I wrote, but I can imagine some might. The operational point probably is that if the referee chose to mention it at all, it means they do have that particular fetish, so just comply if you want approval. But don't "pass it on", if you were to ask my opinion... :)