You will be able to separate those plantlets and prick them out into bigger, deeper containers. I probably wouldn't be looking to keep them indoors but in a sheltered outside space such as a coldframe, cloche or cold greenhouse. I have many seedlings sprouting now in my unheated greenhouse and even outside in the garden pots. Although it looks daunting, tip the whole medium out and carefully prise the little plants apart - they will either keep a portion of soil around the roots or it will fall off...but no matter, the main thing is to replant into some loosely friable and well-drained mix for their next stage of growth which, if cold, will happen very slowly - I have some seedlings which stay minuscule for months until the conditions for growth are right. Don't fret, all is not lost, just be patient, hold the seedlings by the stems and loosen the soil with a small stick, teaspoon or whatever. Pricking out little seedlings is one of the joys of growing from seed. If the space where they germinated was fairly warm, you will have to prepare the seedlings for a life outside by means of a gradual hardening off process over the next 2 weeks or so (inside at night, out in the day, covered if required).