My research was fruitful. It is possible to use JS Grid's server side API, but parts of the client side API are needed as well. Here's how:
On the server, when building the data table containing the grid's data, there needs to be one special column that contains the so called 'row style ID'.
// Create and initialize the data table.
DataTable data = new DataTable();
// Add the normal data columns.
// ...
// Add the column for the row style ID.
data.Columns.Add(new DataColumn(
GridSerializer.DefaultGridRowStyleIdColumnName,
typeof(String)));
// ...
After the data table is created, it needs to be filled with data. The row style ID column (which is referenced by its default name (see DefaultGridRowStyleIdColumnName)) is where you put in your own row style IDs that you want for specific rows.
// Declare dataRow variable.
DataRow dataRow;
// Create new instnace of DataRow.
dataRow = data.NewRow();
// Add regular data to the row.
// ...
// Add the row style ID to the row.
dataRow[GridSerializer.DefaultGridRowStyleIdColumnName] = "MyStyleID";
// Add the current row with data to the data table object.
data.Rows.Add(dataRow);
// Repeat as loop if needed
// ...
The last part is to define the actual row styles you want to use to change the visual appearance of different rows. This part needs to be done in JavaScript on the client side, specifically in the script section where the grid's parameters are defined (in the GridManager's Init method). The StyleManager's RegisterCellStyle method is used to associate a row style ID with an actual row style:
// ...
// Define a row style for MyStyleID.
jsGridParams.styleManager.RegisterCellStyle('MyStyleID', SP.JsGrid.Style.CreateStyle(SP.JsGrid.Style.Type.Cell, { backgroundColor : '#EA3030' }));
// ...
With these parts in place the default visual style of a row can be changed. By defining different row styles and by associating different rows with those styles through their row style ID, you can individually set the style for each row.
Important Note:
For the sake of simplicity this answer's code parts are in close context of the MSDN JS Grid example How to: Create a Basic JS Grid Control
Example screen shot with colored rows: