Bhakoot dosha should not be ignored does not mean that marriage should be avoided. Actually you need to study the Karka of Love and children that is Venus and Jupiter in both the horoscopes. If the Karkas are strong and well positioned , and giving results then bhakoot can be avoided. If the karka of love and children are also afflicted and do not have strength then surely bhakoot should not be avoided. Also you need to take Mangal Dosha, and strength of 7th house and lord for analysing marriage.
Many charts I have seen may not have Bhakoot dosha but their 7th lord is signifying separation then even then marriage will break. I believe that Gun milan is important but Graha milan is more important as it tell us exactly what planets promise in the horoscope.
You may take the Paid service “Horoscope Matching Kundali Milan” for a detailed horoscope matching. The link is given below for your reference.