The assumption that the second (and higher) deprotonation steps are negligible for the calculation of the pH of a polyprotic acid is valid for citric acid.

You can compare this by calculating the exact solution and then stepwise neglect deprotonation steps.

(For the sake of simplicity I write $c(\ce{H+})=x$ and $k_{a,n}=k_n$.)

Exact: $$x=\frac{k_W}{x}+c_0(\ce{H3A})\frac{x^2 k_1+2x k_1 k_2+3 k_1 k_2 k_3}{x^3+x^2 k_1+x k_1 k_2+k_1 k_2 k_3}$$
Neglecting $k_3$: $$x=\frac{k_W}{x}+c_0(\ce{H3A})\frac{x k_1+2 k_1 k_2}{x^2+x k_1+k_1 k_2}$$
Neglecting $k_2$ and $k_3$: $$x=\frac{k_W}{x}+c_0(\ce{H3A})\frac{k_1}{x+k_1}$$

Solving those equations give the following pH values (with super unrealistic high precision):

 - Exact:               **1.24692910**50971560
 - w/o $k_3$:           **1.24692910**65371300
 - w/o $k_2$ and $k_3$: **1.247**0654318802320

As a pH can only be measured precisely within something like $\pm \left(10^{-2}\ldots10^{-3}\right)~\mathrm{pH}$, the calculated pH can be rounded to be 1.247 in every singly case. No matter which deprotonation step was neglected.

So for your case it is negligible. For more general cases I have to look it up and will add it to my answer within the next days.