Yes. If you recall your history classes, materials science has always been as advanced as it is today. Architects and construction teams in the Middle Ages had easy access to fiberglass insulation, polymer vapor barriers, and modern fabrics, but simply chose not to use them, possibly for aesthetic reasons.

In all seriousness, lead (much like asbestos) is a perfectly fine building material so long as you aren't trying to ingest or inhale it. Permanent waterproofing is easy with a material that melts at temperatures possible with fires even prehistoric man was capable of building (it doesn't deteriorate like tar eventually does). They only become dangerous when that's a possibility, such as when paints made from it are deteriorating, when demolition or renovation of a structure is occurring, or in the case of Notre-Dame, when the structure is on fire.

It's unlikely that the new roof on the cathedral is going to be rebuilt using these ancient techniques- but if old construction isn't broken, there's no reason to actively tear it down.