While @Lucia's answer is my favorite, I thought it might be worthwhile to sketch the Plancherel-based argument I alluded to in the above.
First of all, let $\phi:[0,\infty)\to \mathbb{R}$ be such that $\phi(t)$ has fast decay as $t\to \infty$ and fast enough decay as $t\to 0^+$, where "fast enough" means "fast enough for the Mellin transform $\Phi(s)$ of $\phi$ to be defined for $\Re s\geq 0$." Assume as well that $\Phi(s)$ has fast decay as $|\Im s|\to \infty$, and that $\Phi(i t)$ does not vanish on $[1,2]$. It will be enough to show that $$\int_{1-i\infty}^{1+i\infty} \frac{|\Phi(s/T)|^2}{|\zeta(s)|^2} ds = O(T),$$ as the left side is bounded from below by $\gg \int_T^{2 T} \frac{dt}{|\zeta(1+ i t)|^2}$.
(It seems likely that one can obtain a bound of $\gg T$ on the original integral in the same way, but it should also be clear that this method will not yield an asymptotic for the original problem; at least I do not see how it could. At the same time, just carrying out the argument carefully probably gives an asymptotic $c T + o(T)$ rather than just an $O(T)$ in the above statement.)
We know that $\Phi(s/T)$ is the Mellin transform of $T \phi(x^T)$, and so
$n^{-s} \Phi(s/T)$ is the Mellin transform of $x\mapsto T \phi((n x)^T)$. Thus, $\frac{\Phi(s/T)}{\zeta(s)}$ is the Mellin transform of $T F(x)$, where $F(x) = \sum_{n} \mu(n) \phi((n x)^T)$. By Plancherel,
$$\frac{1}{2 \pi} \int_{1-i \infty}^{1+i \infty} \frac{|\Phi(s/T)|^2}{|\zeta(s)|^2} ds = T^2 \int_0^\infty |F(x)|^2 x dx.$$
We see that $F(x)$ is a smoothed sum of $\mu(n)$, essentially supported on an interval $I_T(x) = ((1-O(1)/T)/x,(1+O(1)/T)/x)$. For $x\gg 1$, $F(x)$ will be negligible (and in fact $0$, if $\phi$ is of compact support. For $1/K(T)\leq x \leq 1/T$ (where $K(T)$ will be chosen later), we use a trivial bound $|F(x)| = O(1/(T x))$, and obtain $$T^2 \int_{1/K(T)}^{1/T} |F(x)|^2 x dx \ll \int_{1/K(T)}^{1/T} \frac{dx}{x} = \log \frac{K(T)}{T}.$$
For $1/T\leq x\leq 1$, $F(x)$ will be non-negligible (and bounded by $|\phi|_\infty$) only a proportion $O(1/x T)$ of the time (whenever $I_T(x)$ happens to contain an integer), and so it should be simple to show that
$$T^2 \int_{1/T}^{1} |F(x)|^2 x dx \ll T\int_{1/T}^1 dx = T,$$
which will be our main term. (We can probably get an asymptotic here without much work.)
It remains to consider $F(x)$ for $0<x\leq 1/K(T)$. We want $K(T)$ to be large enough for us to be able to get cancellation on a (smoothed) sum of $\mu(n)$ on an interval of length in the order of $K(T)/T$ centered around $T$. If we are willing to use short-interval results (which are of course completely fine, but rest on zero-free regions, at least if one wants to gain a factor of more than $\log K(T)$, as we need to) then we can set $K(T) = T^4$ (say). If we just want to use a result of Hadamard-de la Vallée-Poussin strength, then we can set $K(T) = \exp(C (\log T)^2)$, and obtain $$T^2 \int_0^{1/K(T)} |F(x)|^2 x dx =
\int_0^{1/K(T)} \frac{1}{e^{c \sqrt{\log(1/x)}}} \frac{dx}{x} \ll 1.$$
Summing up, we get a bound of $O(T)$.
(In the last step, can also use weaker results than what follows from a classical zero-free region. For instance, there are explicit bounds on smooth sums of length $y$ that gain a factor of $C' (\log y)^2$ ($C'$ a constant, often large) with respect to the trivial bound. That is enough; we just need $K(T)$ to be smaller than $T$ (so that $\log K(T)/T$ does not overwhelm $T$ and we also need the gain over the trivial bound to be at least a little larger than $(\log y)$ (so that the integral $\int_0^{1/K(T)} |F(x)|^2 x dx$ converges).