Got there in the end. Here is the proof I used, I thought I'd post it as it was quite fun to prove in the end. I would also appreciate it if anyone can point out errors. Also, apologies for poor presentation I'm fairly new to Latex.
Since q | F_{k} = 2^{2^{k}} + 1 \Leftrightarrow 2^{2^{k}}\equiv -1 (mod q)
Noting that 2^{2^{k}} - 1 = (2^{2^{k-1}} +1)(2^{2^{k-1}} - 1) = F_{k-1}(2^{2^{k-1}} - 1) you can write F_{k} as:
F_{k} = 2^{2^{k}} + 1 + (2 - 2) = 2^{2^{k}} - 1 + 2 = F_{k-1}(2^{2^{k-1}} - 1) + 2 = F_{k-1}F_{k-2}(2^{2^{k-2}} - 1) + 2 = F_{k-1}F_{k-2}...F_{2}F_{1} + 2
So for any l =1,2, ..., k-1 we can write F_{k} as:
F_{k} = F_{k-1}F_{k-2}F_{k-3}...(2^{2^{l-1}} - 1) + 2.
Assume that for some l =1,2,...,k-1 we have 2^{2^{l}}\equiv 1 (mod q), then (2^{2^{l-1}} - 1) = 0 (mod q) and F_{k} - 2 = 0 (mod q ) = F_{k} since q | F_{k}. So 2|q \Rightarrow q=2, but F_{k} = 2^{2^{k}} + 1 is odd, so we have a contradiction. Thus 2^{2^{l}} \not \equiv 1 (mod q) \forall l = 1,...,k since also, already shown that 2^{2^{k}}\equiv -1 (mod q)
Now, since q is prime, using Fermat's Little Theorem 2^{q-1} = 1 (mod q) since q \not | 2.
Also,
F_{k+1} -2 = F_{k}F_{k-1}...F_{2}F_{1} = 0 (mod q) since q | F_{k}. So 2^{2^{k+1}} + 1 - 2 = 0 (mod q) \Rightarrow 2^{2^{k+1}} = 1 (mod q)
Noting that x^a \equiv 1 (mod m) and x^b \equiv 1 (mod m) \Rightarrow x^{gcd(a,b)} \equiv 1 (mod m), we get the result:
2^{gcd(q-1,2^{k+1})} \equiv 1 (mod q)
Now, since gcd(q-1,2^{k+1}) must be a divisor of 2^{k+1} it must be of the form 2^{l} for some l=0,...,k+1 , but it can't be any l = 1,...,k since otherwise 2^{2^{l}}\equiv 1 (mod q) contradicting our earlier result. Also, it can't be 2^{l=0} = 1 since otherwise 2^{gcd(q-1,2^{k+1})} = 2 \equiv 1 (mod q) \Rightarrow q = 1 which is a contradiction, because q is prime.
So, therefore, having exhausted all other possibilities, gcd(q-1,2^{k+1}) = 2^{k+1}, finishing the proof.