Bad news: you have many options
use flatfile transformations: Extract all the data into flatfiles, manipulate them using grep, awk, sed, c, perl into the required insert/update statements and execute those against the target database
PRO: Fast; CON: extremly ugly ... nightmare for maintanance, don't do this if you need this for longer then a week. And a couple dozens of executions
use pure sql: I don't know much about sql server, but I assume it has away to access one database from within the other, so one of the fastes ways to do this is to write it as a collection of 'insert / update / merge statements fed with select statements.
PRO: Fast, one technology only; CON: Requires direct connection between databases You might reach the limit of SQL or the available SQL knowledge pretty fast, depending on the kind of transformation.
use t-sql, or whatever iterative language the database provides, everything else is similiar to pure sql aproach.
PRO: pretty fast since you don't leave the database CON: I don't know t-sql, but if it is anything like PL/SQL it is not the nicest language to do complex transformation.
use a high level language (Java, C#, VB ...): You would load your data into proper business objects manipulate those and store them in the database. Pretty much what you seem to be doing right now, although it sounds there are better ORMs available, e.g. nhibernate
use a ETL Tool: There are special tools for extracting, transforming and loading data. They often support various databases. And have many strategies readily available for deciding if an update or insert is in place.
PRO: Sorry, you'll have to ask somebody else for that, I so far have nothing but bad experience with those tools.
CON: A highly specialized tool, that you need to master. I my personal experience: slower in implementation and execution of the transformation then handwritten SQL. A nightmare for maintainability, since everything is hidden away in proprietary repositories, so for IDE, Version Control, CI, Testing you are stuck with whatever the tool provider gives you, if any.
PRO: Even complex manipulations can be implemented in a clean maintainable way, you can use all the fancy tools like good IDEs, Testing Frameworks, CI Systems to support you while developing the transformation.
CON: It adds a lot of overhead (retrieving the data, out of the database, instanciating the objects, and marshalling the objects back into the target database. I'd go this way if it is a process that is going to be around for a long time.
Building on the last option you could further glorify the architectur by using messaging and webservices, which could be relevant if you have more then one source database, or more then one target database. Or you could manually implement a multithreaded transformer, in order to gain through put. But I guess I am leaving the scope of your question.