What does "thermodynamic equilibrium" mean for an enzyme-substrate complex?
Thermodynamic equilibrium means that:

Rate of forward reaction = Rate of backward reaction

In this case: 

$E + S\xrightleftharpoons[k2]{k1} ES\\ \ \\
 \ \\ \\ at\ equilibrium:\\ \  \ \\ \ k1.[E][S] \tiny{\ (forward\ rate)}\normalsize=  k2.[ES] \tiny\ (backward\ rate)
$

This was the initial assumption in the Michaelis-Menten model.

Later on this was improvised by assuming pseudo-steady state of ES complex. This means that $[ES]$ does not change over time, which is both as a result of its production by the reversible reaction:  $E + S \leftrightharpoons\ ES$ and consumption by the irreversible reaction $\ ES\ \xrightarrow{k3} E+P$

that is:

$k1[E][S]\tiny\ (production)\normalsize=(k2+k3)[ES]\tiny\ (consumption)$