$\newcommand\A{\widetilde{A}}$
$\newcommand\Z{\mathbf{Z}}$
$\newcommand\Q{\mathbf{Q}}$
$\newcommand\rhobar{\overline{\rho}}$
This is in response to the comment of the OP: As far as I can see you are only showing that the stability of $\ker(\rho)$ is a necessary condition for having a lift with stable kernel, but not a sufficient one.
Yes, that is correct. And as far as I can see, your question was "[is] there a lift $\rho$ whose kernel is preserved by $\varphi$" and the above shows that the answer is "no," and moreover will always be no if the kernel of $\rhobar$ is not preserved by $\varphi$. I made no claim that $\ker(\rhobar)$ being preserved by automorphisms implies that there exists a lift with this property. Perhaps this is your actual question?
Question: Suppose that $\ker(\rhobar)$ is preserved by automorphisms of $G_K$. Then can one find a lift $\rho$ such that $\ker(\rho)$ is preserved by automorphisms of $G_K$?
The answer to this question is no, in general.
Let $\A_5$ denote the perfect central extension of $A_5$ by $\Z/2\Z$.
Let $G$ be the semi-direct product of $\Z/2\Z$ by $H = (\A_5)^2$, where the action of $\Z/2\Z$ on $H$ is given by permuting the coordinates. Now suppose that $M/\Q$ is a Galois extension with Galois group $G$. Let $K$ be the corresponding quadratic subfield with fixed field $H$. There is a representation:
$$\rho: G_K \rightarrow \mathrm{Gal}(M/\Q) = H \rightarrow \mathrm{GL}_{6}(\mathbf{C})$$
which factors through the quotient $\A_5 \times A_5$ of $H$ (the latter group has a faithful representation of dimension $2 \times 3$). On one hand, the projective representation $\rhobar$ factors through $A_5 \times A_5$, and so the kernel of $\rhobar$ is Galois over $\Q$. On the other hand, the fixed field of $\ker(\rho)$ is not Galois over $\Q$. Since $\rhobar$ is irreducible, all other lifts are of the form $\rho \otimes \chi$ for some character $\chi$ of $G_K$ (Schur's Lemma). Because $H$ is perfect, the image of such a representation will be $\A_5 \times A_5 \times C$ for some cyclic group, and the same argument as above will apply to show that $\ker(\rho)$ is not normal in $G_{\Q}$.
(To make this complete, one should actually produce an extension of $\Q$ with Galois group $G$, but this should be easily enough to find by taking a generic $\A_5$ extension of some quadratic field.)
There may well be simpler examples, but the motivation behind this particular example is to find a group $H$ with a non-cyclic Schur multiplier with the property that $\mathrm{Out}(H)$ acts non-trivially on $H^2(H,\mathbf{C}^{\times})$.
Edit This is in response to follow up comment of the OP: I'm sorry for not being clear. My question was a 'short hand' for 'is there a lift stable under the automorphism? If the answer is not in general, can we find conditions to ensure the existence of such a lift?'
As noted before, a necessary condition is that the fixed field of $\ker(\rhobar)$ is Galois over $E$, where $E$ is the fixed field of $\Aut(K)$. If $K = E$ this is a sufficient condition. If $K \ne E$, one additional condition that ensures a lift with suitable properties is that the Schur multiplier of the image of $\rhobar$ is trivial, because then there will exist a lift with $\ker(\rhobar) = \ker(\rho)$. So this answers the third version of your question.
Wait, perhaps your question is actually (version 4): give complete necessary and sufficient conditions for the existence of a lift in all circumstances.
Indeed I certainly have some ideas about this, although at this point, I am no longer inclined to work out the details.