The only way I found to make this work correctly when having users non local to the system (e.g. ldap, sssd+ldap, freeIPA) without calling id in a subprocess is by calling the getgrouplist c function (which is called by id eventually after going trough some abstractions):
#!/usr/bin/python
import grp, pwd, os
from ctypes import *
from ctypes.util import find_library
libc = cdll.LoadLibrary(find_library('libc'))
getgrouplist = libc.getgrouplist
# 50 groups should be enought?
ngroups = 50
getgrouplist.argtypes = [c_char_p, c_uint, POINTER(c_uint * ngroups), POINTER(c_int)]
getgrouplist.restype = c_int32
grouplist = (c_uint * ngroups)()
ngrouplist = c_int(ngroups)
user = pwd.getpwuid(2540485)
ct = getgrouplist(user.pw_name, user.pw_gid, byref(grouplist), byref(ngrouplist))
# if 50 groups was not enought this will be -1, try again
# luckily the last call put the correct number of groups in ngrouplist
if ct < 0:
getgrouplist.argtypes = [c_char_p, c_uint, POINTER(c_uint *int(ngrouplist.value)), POINTER(c_int)]
grouplist = (c_uint * int(ngrouplist.value))()
ct = getgrouplist(user.pw_name, user.pw_gid, byref(grouplist), byref(ngrouplist))
for i in xrange(0, ct):
gid = grouplist[i]
print grp.getgrgid(gid).gr_name