If you're performing arati, it suggests you have insufficient faith in God to protect you.

Sage has been used for a long time for spiritual cleansings. If mom wants to do it along with prayer, it's fine.

Good old soap and water and opening the windows is the best method of "cleansing" a house.  There's no "negative energy."  That's superstition.

I suppose it is considered, by some, to be those things. A person's way of seeing things is a reflection of their own mind. I see smudging as it was introduced to me, that is, as a traditional Native American practice. I like the, what I see as symbolic, meaning of smudging, and I find it, and other aspects of their spirituality appealing. If you want to know about smudging, perhaps you should try to see it in the way that a knowledgeable Native American practitioner does, rather than seeing it in the way that someone who is basically ignorant sees it.

There's no such thing as negative energy in a person's house. Especially if they are a Christian. There's more "negative energy" in the world than anything... and you deal with it by keeping faith in God. I wouldn't recommend burning sage, candles, incense or anything. Pray to God, praise him, keep faith in him, and don't worry about darkness.

It's not necessarily witchcraft, but it's pretty close to it.

OK - Nicely superstition is stupid 

how can something said from the Bible be wrong

I do not believe that smudging does anything other than putting smoke into the house.

I may be wrong.

But I may be right.