An instance of CNF-SAT with $k$ variables can easily be written as a 0/1 integer linear program over the same variable set, since a clause such as $x_1 \vee x_3 \vee \neg x_4 \vee \neg x_6$ naturally corresponds to a constraint $x_1 + x_3 + (1-x_4) + (1-x_6) \geq 1$, when all variables are forced to take values $0$ and $1$.
Hence if integer programming in $k$ variables can be solved in time $k^{O(k^\alpha)}$ for some $\alpha < 1$, then CNF-SAT with arbitrarily long clauses can be solved in $k^{O(k^\alpha)} = 2^{O(k^\alpha \cdot \log k)}$, which would contradict the Strong Exponential Time Hypothesis since $c \cdot k^\alpha \cdot \log k < k$ for any constant $c$, $\alpha < 1$, and sufficiently large $k$.