Trees are remarkably resilient. I can remember being frightened of cutting roots as a beginner. Most can cope with loss of up to half the roots at any time so we grow accustomed to cutting roots when repotting bonsai.
Roots that have tips in the air will probably die but any that have the tips in the soil will be fine even if some intermediate parts are exposed. Look up root over rock bonsai to see that roots can be fine growing through the air provided the ends are in soil.
Your tree is small. Plenty of time to go further in future. For this year I would leave it be and get over the fear of repotting then do a better job next spring.
There will be lots of advice to 'put it in the ground or grow box' to get a bigger, thicker trunk but growing small bonsai is also legitimate so you have a choice to keep the small pot.
Hope you understand that junipers do not like being indoors. Definitely keep it outdoors if you hope for it to survive longer than a few weeks.
