What is the best way to test ETLs- Source vs Target data comparision

The current set up that we have for testing ETLs is :

The target Datawarehouse Database is connected to the Source database through a linked server .

QA team has written a script which will read , transform the data from Source database and compare the result with the tables on the data warehouse , column by column for a sample of 100,000 records .

The company policy might take away the linked server connectivity , in which case , there will be no connectivity between the source and target database to do the column by column comparision.

Is there any other way to do this without using any ETL tool ( because that is what being tested)

I can think of a third program like (Python etc) which sets up Database connections to both the Source and Target DBs , downloads the data and does a file comparision or something like that . Any better ideas ?

Are there any tools available for this type of testing ?