I will give an outline of the argument I had in mind from the comments, but leave some details for you to fill in yourself. I ended up taking a slightly different approach (blowing $U$ up instead of shrinking $\mathbb{R}^2$ down) because it felt more direct.
I'll just consider the case where $U=B_\frac{\pi}{2}(0)$, the open ball of radius $\frac{\pi}{2}$ centred at the origin (you should figure out how to adapt this argument/result to the general case). If we use polar coordinates then we can define a homeomorphism $\tau\colon U \to \mathbb{R}^2$ by $\tau (r, \theta) = (tan(r), \theta)$.
However, we want everything to preserve basepoints so we need to fix the elements of $q$. For this purpose choose a closed disk $D\subset U$ centred at the origin with radius $\rho< \frac{\pi}{2}$ such that all of the elements of $q$ are contained in $D$. Now choose a bump function $\psi \colon \mathbb{R} \to I$ such that $\psi((-\rho, \rho)) = 1$ and $\psi((-\frac{\pi}{2},\frac{\pi}{2})^c) = 0$, and define a new homeomorphism $h \colon U \to \mathbb{R}^2$ by
$$ h(r,\theta) = \big(r + (1 - \psi(r))\cdot tan(r),\theta\big)$$
(you can see that this function is injective because it is strictly increasing in the radial coordinate). Then $h$ fixes $D$ pointwise, and there is an isotopy $\iota_U \sim h$ (where $\iota_U$ is the inclusion) given by
$$ H(r,\theta;s) = \big(r + s(1 - \psi(r))\cdot tan(r),\theta\big)$$
which fixes $D$ for all time.
Now let's turn to configuration spaces. If $f\colon X \to Y$ is an injective continuous function then it induces a continuous function $C_n(f) \colon C_n(X) \to C_n(Y)$, by applying $f$ coordinate-wise and noting it is well-defined because you quotient out by the same action on both sides. (Note that if $f$ were not injective then applying it coordinate-wise would not send $F_n(X)$ to $F_n(Y)$.) Moreover if $f$ is a homeomorphism then so is $C_n(f)$.
In particular, for each $s$ our $H_s$ above induces a pointed map $(C_n(U), q)\to (C_n(\mathbb{R}^2), q)$ and these assemble into a homotopy $\tilde{H}\colon C_n(U) \times I \to C_n(\mathbb{R}^2)$ where $\tilde{H}_0 = C_n(\iota_U)$ is the inclusion we're interested in, $\tilde{H}_1 = C_n(h)$ is a homeomorphism, and $\tilde{H}$ fixes $q$ for all time. I.e. our inclusion of configuration spaces is pointed-homotopic to a homeomorphism (in fact it is a pointed homotopy equivalence, where the homotopy inverse is $C_n(h^{-1})$) and therefore the map on braid groups $(\iota_U)_*\colon \pi_1(C_n(U), q) \to \pi_1(C_n(\mathbb{R}^2),q)$ is an isomorphism.
(Caution: we cannot formally say that "$\tilde{H} = C_n(H)$" because it is not the case that $C_n(X\times I) \cong C_n(X) \times I$. You will have to argue more directly that $\tilde{H}$ is continuous with respect to $s$.)
Edit: The above argument seems to generalize to the following statement, which might be enlightening for you to prove:
Suppose $f\colon X \to Y$ is a topological embedding which is isotopic to a homeomorphism, through an isotopy that fixes a set $q\subset X$ of $n$ points. Then the induced function $C_n(f)\colon (C_n(X),q) \to (C_n(Y),q)$ is a pointed homotopy-equivalence.