From your description, I'm not entirely clear if the performance issues you are experiencing are with the draw time of the feature class within ArcGIS or with the process of deleting and inserting of records. Perhaps it is both workflows that are yielding slow behavior.
Two quick questions come to mind right away:
Is the performance of your non-SDE source data the same, better, or worse than that of the SDE data you are describing?
In thinking about the complexity of your polygon features, do they have millions of vertices or only a few per polygon?
You might see better performance with the following sequential steps:
1. TRUNCATE
When connected to your Edit version (which is assumed to be a child version of Default), use the Truncate GP tool to wipe out the records from your polygon feature class. It sounds like you need to clean it out entirely, but correct me if I'm wrong here. Truncate works much more efficiently than a delete operation, but doing this will immediately commit your transaction in the RDBMS without the ability to roll back.
2. LOAD
You can use the Simple Data Loader tool in ArcCatalog or the Load Objects tool in ArcMap to insert the records from your non-SDE source into your target geodatabase. Make sure you're connected to your Edit version when doing this.
3. RECONCILE / POST
Since you loaded data into the Edit version, those changes need to be "moved" into the Default version using the reconcile and post tools within ArcGIS Desktop.
4. COMPRESS
You mentioned a compress earlier, and you are correct in that thought process. After reconcile and post, compress your geodatabase as while connected to your Default version as the SDE user in order to move your adds and deletes to the base table.
5. RDBMS MAINTENANCE TASKS
As you eluded to earlier, performing other RDBMS-related maintenance tasks can help to increase performance. These include analyzing tables and indexes as well as rebuilding indexes. There are many, many other types of database maintenance tasks that can help increase performance and are described online on a variety of sites.
On a related note, I personally do not recommend deleting a feature class and then importing data in order to create a new one... especially if the data you're working with is intended to be versioned. If the data does not need to be versioned, then it is less of a challenge to do this. (Permissions have been the main concern in that specific case, although this might be automatically handled in newer ArcGIS software if the data resides in a feature dataset.) If the data needs to be versioned, then each time you delete the old feature class and add a new one via Import you will need to re-register it as versioned as you discussed already.
It is possible that your performance issues are related to other problems and have nothing to do with the methods you're using to delete and insert new data. Therefore, if the above workflow doesn't help you I would recommend taking a look at your database server's memory, disk I/O stats, and CPU. It could be data-related. Otherwise, it could be network-related. Performance issues are tough to troubleshoot, especially via a forum post. It really could be just about anything that is causing the slow behavior.