I don't think you're alone in that sentiment. Now, I haven't completely cast the brand aside, as I appreciate Eric's style and the one-man nature of his operation. However, the expediency of his shipping process has caused me to reconsider ordering a few items, especially as gifts.
If it continues to concern you, you could take them to a cobbler and have him stitch one side of the tongue to the inside of the upper. It shouldn't be hard for them to line it up with stitching already present.
That's fantastic! It's too bad they don't make a darker brown, but if you want to see how the regular brown will look next to some bourbons, here is a picture. I'm sorry I didn't lace them up, but they're boot laces, and I was just throwing them in there for a color reference. I think they're a little light, but they might work on a boot.
You could try these. They're a little bit narrower and noticeably thicker. They don't really have a dark brown, but they have some options, and the pictures on the site are pretty true to the actual colors. I recommended them in the Alden thread, and I think they would fulfill your wishes. http://www.amazon.com/Strong-Flat-Shoe-Laces-Black/dp/B007BCUI8Y/ref=sr_1_1?ie=UTF8&qid=1387376380&sr=8-1