I thought of a divide-and-conquer approach that might work.
First, in preprocessing you need to insert all numbers less than one half your input size (n/3) into a list.
Given a string: 0000010101000100
(note that this particular example is valid)
Insert all primes (and 1) from 1 to (16/2) into a list: {1, 2, 3, 4, 5, 6, 7}
Then divide it in half:
100000101 01000100
Keep doing this until you get to strings of size 1. For all size-one strings with a 1 in them, add the index of the string to the list of possibilities; otherwise, return -1 for failure.
You'll also need to return a list of still-possible spacing distances, associated with each starting index. (Start with the list you made above and remove numbers as you go) Here, an empty list means you're only dealing with one 1 and so any spacing is possible at this point; otherwise the list includes spacings that must be ruled out.
So continuing with the example above:
1000 0101 0100 0100
10 00 01 01 01 00 01 00
1 0 0 0 0 1 0 1 0 1 0 0 0 1 0 0
In the first combine step, we have eight sets of two now. In the first, we have the possibility of a set, but we learn that spacing by 1 is impossible because of the other zero being there. So we return 0 (for the index) and {2,3,4,5,7} for the fact that spacing by 1 is impossible. In the second, we have nothing and so return -1. In the third we have a match with no spacings eliminated in index 5, so return 5, {1,2,3,4,5,7}. In the fourth pair we return 7, {1,2,3,4,5,7}. In the fifth, return 9, {1,2,3,4,5,7}. In the sixth, return -1. In the seventh, return 13, {1,2,3,4,5,7}. In the eighth, return -1.
Combining again into four sets of four, we have:
1000
: Return (0, {4,5,6,7})
0101
: Return (5, {2,3,4,5,6,7}), (7, {1,2,3,4,5,6,7})
0100
: Return (9, {3,4,5,6,7})
0100
: Return (13, {3,4,5,6,7})
Combining into sets of eight:
10000101
: Return (0, {5,7}), (5, {2,3,4,5,6,7}), (7, {1,2,3,4,5,6,7})
01000100
: Return (9, {4,7}), (13, {3,4,5,6,7})
Combining into a set of sixteen:
10000101 01000100
As we've progressed, we keep checking all the possibilities so far. Up to this step we've left stuff that went beyond the end of the string, but now we can check all the possibilities.
Basically, we check the first 1 with spacings of 5 and 7, and find that they don't line up to 1's. (Note that each check is CONSTANT, not linear time) Then we check the second one (index 5) with spacings of 2, 3, 4, 5, 6, and 7-- or we would, but we can stop at 2 since that actually matches up.
Phew! That's a rather long algorithm.
I don't know 100% if it's O(n log n) because of the last step, but everything up to there is definitely O(n log n) as far as I can tell. I'll get back to this later and try to refine the last step.
EDIT: Changed my answer to reflect Welbog's comment. Sorry for the error. I'll write some pseudocode later, too, when I get a little more time to decipher what I wrote again. ;-)