I solved the issue by first publishing the RDL, then calling into the ReportingService2005 GetItemDataSources() method. I then modified that datasource and subsequently called SetItemDataSources() to save the changes into SSRS. Below is a snippet of the code I accomplished this with:
var reportItem = report.TargetFolder + "/" + report.Name;
var dataSources = new DataSource[0];
dataSources = rs.GetItemDataSources(reportItem);
if (dataSources.Any())
{
var dataSource = (DataSourceDefinition)dataSources.First().Item;
dataSource.CredentialRetrieval = CredentialRetrievalEnum.Store;
dataSource.UserName = SsrsUsername;
dataSource.Password = SsrsPassword;
rs.SetItemDataSources(reportItem, dataSources);
}