Romans 11:36 has DIA + the genitive which can be translated either as "through" or "by." Either translation is able to communicate the notion of intermediate agency, I would say. Colossians 1:16 is also DIA + genitive and Hebrews 2:10 is DIA + the genitive case (DI' hOU). What will determine how one renders the construction should be context or translator preference. But, as I see it, nothing is wrong with communicating agency with "through" or "by." BDAG shows that DIA may be used as a "marker of instrumentality or circumstance whereby someth. is accomplished or effected, by, via, through" (page 224); DIA can also be a "marker of pers. agency, through, by" (BDAG, 225).
In John 1:3, 10; 1 Corinthians 8:6; Colossians 1:16, DIA is used of "Christ as intermediary in the creation of the world" (BDAG, 225).
I examined a number of grammars that I own and one helpful resource I found was A.T. Robertson's A Grammar of the Greek New Testament in the Light of Historical Research. On p. 580, Robertson quotes Delbruck who has "nothing to say" about the origin of DIA. Nevertheless, Robertson proceeds to offer a number of illuminating comments on this Greek preposition, wherein he notes that "there is no doubt about DIA being kin to DUO, DIS. (cf. Sanskrit DVIS, Greek DIS, b = v or U); German ZWEI; English two (fem. and neut.), twain (masc.), twi-ce, twi-light, be-tween, two-fold, etc."