Most cacti have a shallow root system (they store water in their stems/trunks) but depending on the type of cacti and the type of roof you have, damage can still occur.
But from a feng shui standpoint, the cactus plant has positive and negative symbolism. It can represent resilience and protection. It must be placed in an auspicious place though or it could have negative effects (thorniness, antisocial, loner, tough or hardened personality). While cacti gardens can have a beauty all their own, they don't invite closeness. Compare a cacti garden to a lush, green meadow, dotted with colorful, soft-petaled flowers where you might take off your shoes, lie in the grass and touch the flowers.
The cactus is not good in the family corner.
Interesting that you consider the cactus to be planted "naturally" upon your roof. The seed must have been blown there by wind or carried by a bird, which while being a natural occurrence, the roof is not a natural place for a plant.
In feng shui, the roof of a house symbolizes your protection, what you might wear on the top of your head, or your public image. Would you wear a cactus upon your head or your hat?
Part of the protection system of a human psyche is to release and cleanse oneself of emotions which is symbolized by the rain gutter. If the cactus prevents the rain gutter from fulfilling its important purpose, it would good to clear it away.
It probably looks out of place on the roof and will make the roof seem out of balance, both inauspicious scenarios.
Tips for placements for cacti in the home:
*NOT on the bedroom nightstand or in bedrooms generally.
*NOT near where people congregate socially.
*Next to windows, for protection.
*In the wealth corner.
*Outdoors for protection.
Slow-growing cacti can absorb negative energy from the environment but their spines, thorns and prickles can represent a thousand daggers or secret arrows that shoot off negative energy or sha towards people in the room. Most people shun using cacti indoors but they can be used positively with care. Keep them away from the reach of children and pets, group them attractively, and most importantly, love and appreciate them and they will love you back.