I have a super trick for that, that feels a bit like cheating. Make a rover with all the science stuff you have, and the retractable wheels. When retracted, the vehicle is "not grounded" and you are able to perform "while flying" science.
this wheels:
Your payload is not specially big. Possible causes:
1) Your craft is not symetrical, download the KER mod, because otherwise you can't see your torque (tendency to fall to one size)
2) Control is given to a probe that is not pointing upwards.
3) Boosters are tilty in general, provide a lot of thrust but as weight is reduced it moves the center of gravity. Move (or remove) the boosters down.
4) I have clashing feelings about control surfaces in rockets Sometimes they are a must, others a nuisance. Careful using (so much) of those.
Fierce Wolf's post in "...while flying over Kerbin's KSC" science experiments? was marked as the answer