Hmmmmm... I checked my books; here's the ones that include a definition:
According to Rotman's Introduction to the Theory of Groups, 4th Edition,
Definition. If $K$ and $Q$ are groups, then an extension of $K$ by $Q$ is a group $G$ having a normal subgroup $K_1 \cong K$ with $G/K_1\cong Q$.
Same definition appears in D.J.S. Robinson's A Course in the Theory of Groups, 2nd Edition.
Marshall Hall's The Theory of Groups states at the beginning of Chapter 15 ("Group Extensions and Cohomology of Groups"):
Generally speaking, any group $G$ which contains a given group $U$ as a subgroup is called an extension of $U$. [...] Here, however, we shall consider only cases in which $U$ is normal in $G$.
He does not seem to define extension in general, but he does say later
Let us suppose that all factors $(u,v)$ in an extension of a group $A$ by a group $H$ lie in the center $B$ of $A$. Then we shall say that $E[A,H,a^u,(u,v)]$ is a central extension of $A$ by $H$.
In the notation that Hall has established, $E[A,H,a^u,(u,v)]$ represents a group in which $A$ is normal, and the quotient modulo $A$ is isomorphic to $H$. So this agrees with the nomenclature in Rotman and Robinson (the book was written in 1959).
Scott's Group Theory (published in 1964), defines:
An extension of $H$ by $F$ is an exact sequence
$$1\to H\to G\to F\to E.$$
On the other hand, Isaacs' Finite Group Theory has the opposite convention (p 66):
Given groups $N$ and $H$, a group $G$ is said to be an extension of $H$ by $N$ if there exists $N_0\triangleleft G$ such that $N_0\cong N$ and $G/N_0\cong H$.
He does note, however:
As we mentioned, however, this use of prepositions is sometimes reversed in the literature, so readers should attempt to determine the precise meaning from the context.
Bourbaki (Algebra I.6.1) gives:
Definition. Let $F$ and $G$ be two groups. An *extension of $G$ by $F$ * is a triple $\mathscr{E}=(E,i,p)$, where $E$ is a group, $i$ is an injective homomorphism of $F$ into $E$ and $p$ is a surjective homomorphism of $E$ onto $G$ such that $\mathrm{Im}(i)=\mathrm{Ker}(p)$.
(That is, the usage agrees with Isaacs)
This does not really answer your question about the history; but it does show that both usages are common in the literature, and that the one you call "consistent with everyday English" has been around for at least fifty years or more. I would try to take a look at Schreier's original paper on factor sets and extensions to see which use was original, and which one was introduced later...
Added. I thought about it some more; here's a guess:
If you think of groups as sets with a binary operation on it, then it makes more sense to think of an extension
$$1\to N \to G\to Q\to 1$$
as "an extension of $N$ by $Q$", because $G$ "extends" $N$ in the sense that it contains (a copy of) $N$, and the operation on $G$ is an extension (in the function sense) of the operation on $G$.
However, groups were not originally thought of this way. Originally, groups were objects that acted on sets. (Burnside calls the elements of a group "operations"). If you have an action of $Q$ on a set $X$, then given an extension
$$1\to N\to G\to Q\to 1$$
there is a natural way to extend that action to all of $G$; by contrast, if you have an extension as above and an action of $N$, it may be impossible to "extend it" to an action of $G$. As an example, the natural action of $S_6$ on $\{1,2\ldots,6\}$ cannot be extended to $\mathrm{Aut}(S_6)$, even though we have an extension
$$1 \to S_6 \to \mathrm{Aut}(S_6)\to C_2\to 1.$$
Here, if you think of groups as "operations on a set", it makes more sense to think of $G$ as "extending" the set of operations from $Q$ to $G$.
So thinking in terms of actions (as you would if you do a lot of representation theory or character theory, which is what Isaacs does, for instance, or what Ken Brown does in Cohomology of Groups), then the terminology that calls $G$ an extension of the quotient by the kernel makes more sense. Thinking in terms of sets with an operation on it makes it so that it makes more sense to call $G$ an extension of the kernel by the quotient.
Again, this is just an (informed) guess; looking at Schreier's paper would likely settle which one was first or why.