Maximal intransitive groups will be $S_a\times S_b$ and have comparatively small index. I think once $d>6$ (otherwise there is a small number effect) the maximal subgroup of maximal index will always be transitive: If $d$ is prime, $AGL(1,d)$ is transitive, maximal, of larger index; if $d=a\cdot b$, then $S_a\wr S_b$ is transitive, maximal of larger index. (To show this one only needs to estimate $x!\cdot (n-x)!$ versus $a!^b\cdot b!$.)
The question on what the largest index is will depend on properties of $d$, as it often will be an almost simple group, and even the sporadic groups can come in. For example if $d$ is prime it will typically be $AGL(1,p)$. If $d-1$ is prime, I think $PGL(2,p-1)$ will be maximal of largest index.
On the other hand for some degrees (e.g. 33,34) no relevant simple groups, or in fact primitive groups of large index, exist and an imprimitive wreath product becomes the best option.
So as a generic answer I think $a!^b\cdot b!$ with $n=ab$, $a$ the smallest prime divisor, is the best estimate one can hope for.
The relevant paper is:
Liebeck, Martin W.(4-LNDIC); Praeger, Cheryl E.(5-WA); Saxl, Jan(4-CAMBC)
A classification of the maximal subgroups of the finite alternating and symmetric groups.
J. Algebra 111 (1987), no. 2, 365–383.
A GAP program to find the indices for small degrees is:
for i in [2..100] do