Obviously, the combination of linestage gain, plus the MC stage gain, and the sensitivity of your amplifier are too much for use with the Helikon. The Helikon is not a high output MC, but it is not low output either. Use the MM stage as you have done, there is no way this physically harms anything.
The only issue is that MM stages tend to have adjustment capabilities suited for MM cartridges (e.g., adjustable capacitive loading and fixed 47k ohm resistive loading). MC cartridges are insensitive to capacitive loading so any adjustable setting of capacitive loading will not do much. In order to change the resistive loading, you will have to probably add your own resistors. This can be done by experimenting with good, high quality low wattage resistors. You could open the preamp up and solder the resistors on to the inside of the RCA jack (between the center pin and the outer part of the jack).
