Efficient way to ensure unique rows in SQLite3

I am using SQLite3 in one of my projects and I need to ensure that the rows that are inserted into a table are unique with regard to a combination of some of their columns. In most cases the rows inserted will differ in that respect, but in case of a match the new row must update/replace the existing one.

The obvious solution was to use a composite primary key, with a conflict clause to handle collisions. Thefore this:

CREATE TABLE Event (Id INTEGER, Fld0 TEXT, Fld1 INTEGER, Fld2 TEXT, Fld3 TEXT, Fld4 TEXT, Fld5 TEXT, Fld6 TEXT);

became this:

CREATE TABLE Event (Id INTEGER, Fld0 TEXT, Fld1 INTEGER, Fld2 TEXT, Fld3 TEXT, Fld4 TEXT, Fld5 TEXT, Fld6 TEXT, PRIMARY KEY (Fld0, Fld2, Fld3) ON CONFLICT REPLACE);

This does indeed enforce the uniqueness constraint as I need it to. Unfortunately, this change also incurs a performance penalty that is way beyond what I expected. I did a few tests using the sqlite3 command line utility to ensure that there is not a fault in the rest of my code. The tests involve entering 100,000 rows, either in a single transaction or in 100 transactions of 1,000 rows each. I got the following results:

                                | 1 * 100,000   | 10 * 10,000   | 100 * 1,000   |
                                |---------------|---------------|---------------|
                                | Time  | CPU   | Time  | CPU   | Time  | CPU   |
                                | (sec) | (%)   | (sec) | (%)   | (sec) | (%)   |
--------------------------------|-------|-------|-------|-------|-------|-------|
No primary key                  | 2.33  | 80    | 3.73  | 50    | 15.1  | 15    |
--------------------------------|-------|-------|-------|-------|-------|-------|
Primary key: Fld3               | 5.19  | 84    | 23.6  | 21    | 226.2 | 3     |
--------------------------------|-------|-------|-------|--