Actually I've found another – slightly different – lyrics for the same song here: http://www.angolotesti.it/A/testi_canzoni_antonio_mungari_64702/testo_canzone_laura_non_ce_1111998.html.
In this version, which by the way is what I understood by listening/meaning, the sentence is:
Solo Laura è la mia coscienza
This would mean that this sentence is unlinked to the previous one, and with this logic "c'è" is perfectly correct.
"C'è" can be translated with "there is" with the implied meaning of "there is something". You can consider it as a figure of speech, the implied "something" can (and should) remain untold because love is a very personal thing, therefore there isn't a specific something for everyone, but without any doubt there is something between love and affection.
Ma tra bene ed amore qualcosa c'è
But between good and love there is something