Replace Delayed shouldn't have any major drawbacks. The advanatge of it is that your update script will finish quicker, the downside is it will mean the update could take a bit longer to actually apear on the site.
The documentation does say that it could take forever for a delayed update to actually take place, but since product databases are mainly read and probably only written to by the update routine that shouldn't be a problem. It is much more likly that its the fulltext index that is starting to bog down.
Creating a new table would probably be quickest if you are not using autnumber columns to point to products (as these would change).
The other thing to do is make sure you are inserting products in batches rather than one query per item as that is massivly faster. i.e do
INSERT INTO table VALUES ('name1','desc1'),('name2','desc2'),('name3','desc 3');
rather than
INSERT INTO table VALUES ('name1','desc1');
INSERT INTO table VALUES ('name2','desc2');
INSERT INTO table VALUES ('name3','desc3')
See speed of insert statements which also applies to replace statements.
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