Did she perform a structural analysis to determine if you have an imbalance? If not then she's just guessing.
Excluding one area and isolating another is a great way to develop the opposite imbalance.
Why not use compound movements that involve the hamstrings, glutes and quads such as a deep squat.
If the concern is soreness interfering wth running then why run at all? Running interferes with running...especially hard running.
What exercises is she having you do? The hamstrings function both as a knee flexor AND as a hip extensor. This powerful hip extension can be seen in the running stride, especially sprinters, as such the hamstring has been called the "speed muscle".
If you truely have an imbalance I would suggest this:
A1) Squat 2 sets of 10, submax
A2) Leg Curl 2-1 (ie: Curl the weight with two legs, slowly let it back down with 1) 2 sets of 4-6
A3) RDL 2 sets of 10, submax
Most people, not just runners, tend to be very quad dominant just due to daily activities like walking. Optimally the hamstrings should be 80% as strong as the quads, but this will vary greatly across difference sports and it can be as high as 100% as strong as the quads. Most untrained people are closer to 60%. To determine strength ratio you'll need a seated leg curl and a seated leg extension and they need to be of the same brand. Just make sure you are working through an equal range of motion and through proper form. Warm up with a couple light sets then select a weight on the leg extension in which you can perform around 5 repetitions to failure. This may take a couple tries, make sure to rest a good 2-3 minutes between attempts. If finding this "5 rep max" takes more than 5 total sets (including warmup) then try again another day. Once you find your "5 rep max" on the leg extension do the same for the leg curl.
Alan