Let $p:\mathbb{R}^6\to T^3\times T^3$ be the universal covering map, which I consider as reducing each coordinate mod $1$. Consider the pre-image $p^{-1}(\Delta)\subset\mathbb{R}^6$. This is the set of $(t_1,\ldots,t_6)\in\mathbb{R}^6$ such that $(t_4,t_5,t_6)-(t_1,t_2,t_3)\in\mathbb{Z}^3$. In other words,
$$
p^{-1}(\Delta) \cong \mathbb{R}^3\times\mathbb{Z}^3,
$$
where the homeomorphism is given by $(t_1,t_2,t_3,t_1+n_1,t_2+n_2,t_3+n_3)\mapsto (t_1,t_2,t_3,n_1,n_2,n_3)$ ($t_i\in\mathbb{R}, n_i\in\mathbb{Z}$). Using this, we can retract $\mathbb{R}^6$ "diagonally" onto $\mathbb{R}^3$ in a way that retracts $p^{-1}(\Delta)$ onto $\mathbb{Z}^3\subset\mathbb{R}^3$. Then as $\mathbb{R}^3 - \mathbb{Z}^3$ is simply connected, we see that $\mathbb{R}^6-p^{-1}(\Delta)$ is also simply connected, so $\mathbb{R}^6-p^{-1}(\Delta)$ is the universal cover of $T^3\times T^3-\Delta$. The deck transformations of the two covers are the same (as the preimages of points in $T^3\times T^3-\Delta$ are the same), so $\pi_1(T^3\times T^3-\Delta)=\pi_1(T_3\times T_3)=\mathbb{Z}^6$.
It is worth noting why this approach falls apart for the $T^1$ case you describe: the preimage of $T^1\times T^1-\Delta$ is not connected. Also, in terms of your specific question:
Can this process be generalized to the higher-dimensional case?
I tried this as well and didn't get all the way there. My idea was to think of the cylinder you found as a fiber bundle, where the base is one of the $T^1$, and the fiber is $T^1-\{point\}$. In that case, the fact that $T^1-\{point\}$ is contractible makes it easier, but $T^3-\{point\}$ isn't (see Presentation of the fundamental group of a manifold minus some points ), so the same process only got so far. Specifically:
(using notation $\mathbf{t}=(t_1,t_2,t_3) \in [0,1)^3$ as coordinates for $T^3$)
Pick an arbitrary $\mathbf{x}\in T^3$ with $\mathbf{x}\neq (0,0,0)$, and define $Y=\{(\mathbf{t},\mathbf{t}+\mathbf{x})\in T^3\times T^3-\Delta : \mathbf{t}\in T^3 \}$ (addition is mod $1$). Define $\pi : T^3\times T^3-\Delta\to Y$ by $\pi(\mathbf{t},\mathbf{s})=(\mathbf{t},\mathbf{t}+\mathbf{x})$. With a little work, you can see that $\pi$ makes $T^3\times T^3-\Delta$ into a fiber bundle over $Y \cong T^3$ with fiber $T^3-\{point\}$. The resulting exact sequence yields
$$
\cdots\to\underset{=0}{\pi_2(Y)}\to\underset{=\mathbb{Z}^3}{\pi_1(T^3-\{pt\})}\to
\pi_1(T^3\times T^3-\Delta)\to\underset{=\mathbb{Z}^3}{\pi_1(Y)}\to\underset{=0}{\pi_0(T^3-\{pt\})}\to\cdots
$$
This is consistent with the answer given above, but I don't see how it is enough to finish it off.