The halting problem doesn't really tell you anything about whether you can prove that a TM recognises a given language.
We can prove that the TM recognises $\{0^n1^m : n \geq 1\}$ using the definition of $L(M)$ and $\mapsto_M$.
One thing to note is that the machine is deterministic, so for each state and character there's at most one transition.
Therefore for each input $w$ there's only one sequence of IDs (one computation) we need to consider to decide if $w \in L(M)$.
These proofs can get very long since there are a lot of cases to consider, so I'll just give a rough sketch.
For simplicity we'll write $\mapsto$ instead of $\mapsto_M$, note the following:
Lemma 1: $X^kq_00^nY^k1^m \mapsto^* X^{k + 1}q_00^{n - 1}Y^{k + 1}1^{m - 1}$ for $k, n, m \in \mathbb{N}; n,m \geq 1$ using only states $q_0, q_1, q_2 \notin F$.
This can be proven by applying the definitions of $\mapsto$ and $M$.
A corollary of Lemma 1 is that for $n \geq m$
$$X^kq_00^nY^k1^m \mapsto^* X^{k + m}q_00^{n - m}Y^{k + m}$$
and for $m \geq n$
$$X^kq_00^nY^k1^m \mapsto^* X^{k + n}q_0Y^{k + n}1^{m - n}$$
using only transitions through $q_0, q_1$ and $q_2$.
From this it follows that for all $n \in \mathbb{N}; n \geq 1$
$$\underbrace{q_00^n1^n}_{=\ X^0q_00^nY^01^n} \mapsto^* X^nq_0Y^n \mapsto X^nYq_3Y^{n - 1} \mapsto^* X^nY^nq_3B \mapsto X^nY^nBq_4B$$
with $q_4 \in F$, so by definition $0^n1^n \in L(M)$.
Now assume that $w \in \Sigma^*; w \notin \{0^n1^n : n \geq 1\}$, then one of the following cases must be true:
- $w = \varepsilon$ or $w = 1x$ for $x \in \Sigma^*$, then $M$ on $w$ directly halts in $q_0 \notin F \Rightarrow w \notin L(M)$.
- $w = 0^n$ for $n \in \mathbb{N}; n \geq 1$, then
$$q_0w \mapsto Xq_10^{n - 1} \mapsto^* X0^{n - 1}q_1B$$
so the machine halts in $q_1$ without ever entering a final state.
Thus $w \notin L(M)$.
- $w = 0^n1^m$ for $n, m \geq 1; n \neq m$, if $n > m$ then by the corollary of Lemma 1
$$q_0w \mapsto^* X^mq_00^{n - m}Y^m \mapsto^* X^{m + 1}0^{n - m - 1}Y^mq_1B$$
so $M$ halts in $q_1$ without having entered a final state.
If $m > n$ then again by Lemma 1
$$q_0w \mapsto^* X^nq_0Y^n1^{m - n} \mapsto^* X^nY^nq_31^{m - n}$$
so $M$ halts in $q_3$ without having entered a final state.
Thus $w \notin L(M)$.
- $w = 0^n1^m0x$ for $n, m \geq 1$ and $x \in \Sigma^*$, $w \notin L(M)$ can be proven similar to the cases above by considering $n = m$, $n > m$ and $m > n$.
So $w \in \{0^n1^n : n \geq 1\} \iff w \in L(M)$, thus $L(M) = \{0^n1^n : n \geq 1\}$.