It sounds like you could do with a join so you're relating the meta information to the right posts.
SELECT
post.post_title,
meta.meta_value
FROM wp_posts AS post
LEFT JOIN wp_postmeta AS meta
ON post.post_id = meta.post_id
WHERE post.post_type = 'product'
AND meta.meta_key IN ('_sku', '_price')
Example results:
post_title | meta_value
--------------|-----------
Cheddar | CHE001
Cheddar | 2.45
Red Leicester | CHE002
...
This assumes that the id column in wp_posts is post_id.
It's important to note that this will return up to two rows for each post, depending on whether it has a meta row for _sku and _price). If you need the data all on the same row (as you might for your export) you might need something like this instead:
SELECT
post.post_title,
metaSku.meta_value AS sku,
metaPrice.meta_value AS price
FROM wp_posts AS post
LEFT JOIN (
SELECT
*
FROM wp_postmeta
WHERE meta_key = '_sku'
) AS metaSku
ON post.post_id = metaSku.post_id
LEFT JOIN (
SELECT
*
FROM wp_postmeta
WHERE meta_key = '_price'
) AS metaPrice
ON post.post_id = metaPrice.post_id
WHERE post.post_type = 'product'
Example results:
post_title | sku | price
--------------|--------|------
Cheddar | CHE001 | 2.45
Red Leicester | CHE002 |
...
I hope this helps.