Looking good.

meikyo, daijs, prog, gg5

I agree. This is what I'd go with.
Added sense.

@@ -29,0 +30,2 @@
+<pos>&vt;</pos>
+<pos>&vi;</pos>
@@ -36,0 +39 @@
+<pos>&vt;</pos>
@@ -40,0 +44,7 @@
+<pos>&vt;</pos>
+<gloss>to welcome (a proposal, advice, etc.)</gloss>
+<gloss>to take kindly to</gloss>
+</sense>
+<sense>
+<pos>&v5b;</pos>
+<pos>&vi;</pos>
@@ -42 +52,4 @@
-<gloss>to gratefully accept</gloss>
+<s_inf>as よろこんで...</s_inf>
+<gloss>to do with pleasure</gloss>
+<gloss>to do gladly</gloss>
+<gloss>to be happy (to do)</gloss>

No comment on senses etc. but it seems weird to me to not include transitivity tags.

Thanks for the submission. I really think that in this case the decision we made in 2012 to avoid attempting to classify the usage into transitive/intransitive groupings and set up senses accordingly was the right one. I think the previous sense split based on the core meanings was more appropriate. I'll put it back that way, and add "to rejoice".

@@ -30 +30,3 @@
-<pos>&vt;</pos>
+<gloss>to be delighted</gloss>
+<gloss>to be glad</gloss>
+<gloss>to be pleased</gloss>
@@ -31,0 +34,3 @@
+</sense>
+<sense>
+<pos>&v5b;</pos>
@@ -36,8 +40,0 @@
-<pos>&vi;</pos>
-<gloss>to be delighted</gloss>
-<gloss>to be glad</gloss>
-<gloss>to be pleased</gloss>
-</sense>
-<sense>
-<pos>&v5b;</pos>
-<pos>&vt;</pos>

GG5, JWN, daijr, daijs, meikyo, 広辞苑第六版, 新明解国語辞典第五版

Proposals
1: Classify [1], [2] and [3] as transitive, intransitive and *transitive respectively. 
Reasoning: While the strict classification of the verb as either transitive or ambitransitive differs across the Japanese sources that do explicitly make that demarcation, this should cover all grounds. 
 *This one might have reason to remain neutral.

2: Further translation of [2]: to rejoice. Translation supported by both GG5 and JWN.

3: Inversion of [1] and [2]. 
Reasoning: Firstly, of the three referents that did state transitivity: 1 was transitive, 1 was ambitransitive and 1 was intransitive; however, even the one that said intransitive still used example sentences with を.
Out of those of the remainder which did not: 2 suggest either ambitransitive or transitive based on use of を in example sentences and transitive constructions in all but one of definitions across both. GG5 did use example sentences with を but lacks definitions in Japanese. And the last, JWN, uses transitive structures for the definitions but has no example sentences.
Based on the above I would say that the overwhelming majority of instances tends to either transitivity or ambitransivity, with only one clearly supporting exclusive intransitivity.

Secondly, there seems to be no circumstance under which a supposedly intransitive variant cannot be interpreted as a transitive verb with an omitted object.
Thirdly, If this is true then assuming transitivity will still deliver you the same semantic content of what would be the counterpart, but the same is not true of the opposite, therefore the former takes precedence over the latter.
Lastly, the previous three points when joined not only seem to indicate a preference for the transitive hypothesis but may also substantiate forsaking the intransitive hypothesis entirely.

@@ -29,0 +30,7 @@
+<pos>&vt;</pos>
+<gloss>to rejoice</gloss>
+<gloss>to congratulate</gloss>
+</sense>
+<sense>
+<pos>&v5b;</pos>
+<pos>&vi;</pos>
@@ -36,4 +43 @@
-<gloss>to congratulate</gloss>
-</sense>
-<sense>
-<pos>&v5b;</pos>
+<pos>&vt;</pos>